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Genomatix gmbh transfac program
Transfac Program, supplied by Genomatix gmbh, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Related Articles

Mutagenesis:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Binding Assay:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Selection:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Quantitative Proteomics:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Control:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Expressing:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Sequencing:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Luciferase:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Plasmid Preparation:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Construct:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Activity Assay:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Immunoprecipitation:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Negative Control:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Amplification:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Quantitative RT-PCR:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Western Blot:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

Transfection:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.

In Silico:

Article Title: Profound hyperglycemia in knockout mutant mice identifies novel function for POU4F2/Brn-3b in regulating metabolic processes
Article Snippet: Genomatix Transfac analysis identified multiple V$BRNF sites in the mouse GLUT4 promoter sequences that could act as potential binding sites for Brn-3b transcription factor ( ).

Article Title: Detection of genetic variation and activity analysis of the promoter region of the cattle tRNA-modified gene TRDMT1
Article Snippet: The combination of TRANSFAC and Genomatix found that the G > C mutation may cause a difference in binding between the transcription factor Sp1, the pleomorphic adenoma gene (PLAG1), the zinc finger protein (ZNF35) and the bone marrow zinc finger 1 factor (MZF1) transcription factor (Figs. 3 and 4).

Article Title: Heat shock factor 2 is a stress-responsive mediator of neuronal migration defects in models of fetal alcohol syndrome
Article Snippet: Transfac (http://www.gene.regulation.com) Genomatix (http://www.genomatix.de) iHOP (http://www.ihop-net.org) ENSEMBL (http://ensembl.org) These web sites were used for the search of HSE in HSF2 target genes or primer design.

Article Title: CCAAT-enhancer binding protein (C/EBP) β regulates insulin-like growth factor (IGF) 1 expression in porcine liver during prenatal and postnatal development.
Article Snippet: IGF1 expression regulation attracts numerous interests because of its important role during mammalian growth and development.. Domestic pig can be used as a valuable animal model to investigate human development since they share the high similarity in general physiology and metabolism.. In this study, we examined the expression pattern of IGF1 and found it associated with liver C/EBP b expression pattern in porcine liver during embryonic and postnatal development.

Article Title: Hormonal regulation of platypus Beta-lactoglobulin and monotreme lactation protein genes.
Article Snippet: Endocrine regulation of milk protein gene expression in marsupials and eutherians is well studied.. However, the evolution of this complex regulation that began with monotremes is unknown.. Monotremes represent the oldest lineage of extant mammals and the endocrine regulation of lactation in these mammals has not been investigated.

Article Title: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells.
Article Snippet: SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells Sumeyye Aydogan Turkoglu, Feray Kockar PII: S0378-1119(15)01004-5 DOI: doi: 10.1016/j.gene.2015.08.035 Reference: GENE 40782 To appear in: Gene Received date: 19 February 2015 Revised date: 30 June 2015 Accepted date: 18 August 2015 Please cite this article as: Aydogan Turkoglu, Sumeyye, Kockar, Feray, SP1 and USF differentially regulate ADAMTS1 gene expression under normoxic and hypoxic conditions in hepatoma cells, Gene (2015), doi: 10.1016/j.gene.2015.08.035 This is a PDF file of an unedited manuscript that has been accepted for publication.. As a service to our customers we are providing this early version of the manuscript.. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form.

Article Title: Functional promoter variants in sphingosine 1-phosphate receptor 3 associate with susceptibility to sepsis-associated acute respiratory distress syndrome
Article Snippet: ARDS-Associated S1PR3 Promoter SNPs Modify Nuclear Transcription Factor Binding Affinity In silico analysis using TRANSFAC and Genomatix revealed that Homo sapiens caudal type homeobox transcription factor 1 (Cdx1) was the only transcription factor binding to S1PR3 promoter and potentially interrupted by −1899G (rs7022797), resulting in loss of Cdx1 binding efficiency compared with the −1899T allele.



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21 target genes of Hypoxia-inducible factor 1α (HIF-1α) out of 216 DEGs in diabetic mice through  TRANSFAC  ® .

Journal: Molecules

Article Title: Therapeutic Effects of HIF-1α on Bone Formation around Implants in Diabetic Mice Using Cell-Penetrating DNA-Binding Protein

doi: 10.3390/molecules24040760

Figure Lengend Snippet: 21 target genes of Hypoxia-inducible factor 1α (HIF-1α) out of 216 DEGs in diabetic mice through TRANSFAC ® .

Article Snippet: The software program, TRANSFAC ® (Qiagen N.V., Valencia, CA, USA), was used to select the target genes of HIF-1α.

Techniques: Binding Assay, Membrane, Ubiquitin Proteomics