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Genomatix gmbh microarray raw data analysis
Microarray Raw Data Analysis, 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
https://www.bioz.com/product/microarray+data+analysis+raw+data/microarray/pm20491563-124-14-15
Average 90 stars, based on 1 article reviews
microarray raw data analysis - by Bioz Stars, 2026-09
90/100 stars

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Microarray:

Article Title: Mining Affymetrix microarray data for long noncoding RNAs: altered expression in the nucleus accumbens of heroin abusers
Article Snippet: Differential expression of these lncRNAs was validated by qRT-PCR ( ) and positively correlated with the previous Affymetrix microarray data ( ). .. A subsequent group-wise analysis of the microarray data (performed with Genomatix ChipInspector) similarly identified changes in these four lncRNAs as well as an additional upregulated lncRNA (EMX2OS, log2fold change=0.35; not validated by RT-PCR due to exhaustion of sample). ..

Article Title: The differentiation and gene expression profile of human dental follicle cells.
Article Snippet: Human dental follicle cells (DFCs) are progenitor cells.. Recent studies supposed that osteogenic differentiation of DFCs is controlled by growth factors such as BMP2 and IGF2, but their infl uence on the differentiation of DFCs has not been investigated in detail.. We examined DFCs after the induction of osteogenic differentiation with BMP2, IGF2 and a standard osteogenic differentiation medium (ODM) with dexamethasone.

Article Title: Transcription Factors as the “Blitzkrieg” of Plant Defense: A Pragmatic View of Nitric Oxide’s Role in Gene Regulation
Article Snippet: .. To find this, Palmieri et al. [ ] searched for a common TFBS in the promoter region of NO-regulated genes based on microarray analyses using Genomatix, Gene2Promoter, and MatInspector. ..

Article Title: Microarrays: quality control.
Article Snippet: .. “The program’s first line of analysis is literature” explains Martin Seifert, vice-president of microarray business at Genomatix. ..

Article Title: Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis
Article Snippet: .. Overlap between GW7647-induced PPARα binding and GW7647-induced changes in expression. ( A ) Significant induction of PPARα targets by GW7647 treatment. ( B ) Number of genes significantly altered upon GW7647 treatment as determined by microarray analysis using criteria: fold change >1.2 and q -value <0.05. ( C ) Overlap between genes assigned to GW7647-induced PPARα binding regions and genes altered after treatment with GW7647 as determined by transcriptomics. ( D ) Percentage of GW7647-induced PPARα binding regions linked to either up- or down-regulated genes that contain at least one V$PERO site, as determined using Genomatix. .. Similar analysis was done for all GW7647-induced PPARα binding regions as well as a control set of promoter regions in the Genomatix promoter database with similar size range as the binding regions identified by ChIP-chip (1000–1500 bp).

Article Title: Summary of Recent Deal Activity
Article Snippet: Companies Type of deal Details Almirall Prodesfarma, R&D agreement Spanish company Almirall Prodesfarma has entered into a collaborative agreement with Sareum Sareum to conduct protein structure determination projects to support accelerated drug-discovery programs at Almirall.. Sareum will use its skills in high-throughput protein expression, purification and structure determination with the aim of elucidating the precise nature of how Almirall’s potential drug candidates interact with their target protein.. This information will assist Almirall’s scientists in their design of new and improved therapeutics against inflammatory diseases.

Article Title: Summary of Recent Deal Activity
Article Snippet: Companies Type of deal Details Agilent Technologies, R&D agreement Ingenuity Systems and Agilent Technologies have signed an agreement to establish Ingenuity Systems integration between Agilent’s GeneSpring Analysis Platform and Ingenuity Pathways Analysis.. Genomics researchers will be able to easily exchange data between both applications, leveraging each system’s ability to analyze high-volume gene-expression data and to perform advanced biological pathway analysis.. The GeneSpring Analysis Platform integrates data and results from multiple measurement technologies, providing comprehensive statistical analysis, data mining and visualization tools.

Article Title: Regulatory networks: linking microarray data to systems biology.
Article Snippet: Gene regulation and aging are intrinsically linked and these links often reach directly to transcription factors and their actions in gene regulation.. However, it is very difficult to follow all the individual directions such factors can affect.. Therefore, the opposite approach became more popular recently, i.e. observing the endpoints of all these actions.

Reverse Transcription Polymerase Chain Reaction:

Article Title: Mining Affymetrix microarray data for long noncoding RNAs: altered expression in the nucleus accumbens of heroin abusers
Article Snippet: Differential expression of these lncRNAs was validated by qRT-PCR ( ) and positively correlated with the previous Affymetrix microarray data ( ). .. A subsequent group-wise analysis of the microarray data (performed with Genomatix ChipInspector) similarly identified changes in these four lncRNAs as well as an additional upregulated lncRNA (EMX2OS, log2fold change=0.35; not validated by RT-PCR due to exhaustion of sample). ..

Binding Assay:

Article Title: Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis
Article Snippet: .. Overlap between GW7647-induced PPARα binding and GW7647-induced changes in expression. ( A ) Significant induction of PPARα targets by GW7647 treatment. ( B ) Number of genes significantly altered upon GW7647 treatment as determined by microarray analysis using criteria: fold change >1.2 and q -value <0.05. ( C ) Overlap between genes assigned to GW7647-induced PPARα binding regions and genes altered after treatment with GW7647 as determined by transcriptomics. ( D ) Percentage of GW7647-induced PPARα binding regions linked to either up- or down-regulated genes that contain at least one V$PERO site, as determined using Genomatix. .. Similar analysis was done for all GW7647-induced PPARα binding regions as well as a control set of promoter regions in the Genomatix promoter database with similar size range as the binding regions identified by ChIP-chip (1000–1500 bp).

Expressing:

Article Title: Profiling of promoter occupancy by PPARα in human hepatoma cells via ChIP-chip analysis
Article Snippet: .. Overlap between GW7647-induced PPARα binding and GW7647-induced changes in expression. ( A ) Significant induction of PPARα targets by GW7647 treatment. ( B ) Number of genes significantly altered upon GW7647 treatment as determined by microarray analysis using criteria: fold change >1.2 and q -value <0.05. ( C ) Overlap between genes assigned to GW7647-induced PPARα binding regions and genes altered after treatment with GW7647 as determined by transcriptomics. ( D ) Percentage of GW7647-induced PPARα binding regions linked to either up- or down-regulated genes that contain at least one V$PERO site, as determined using Genomatix. .. Similar analysis was done for all GW7647-induced PPARα binding regions as well as a control set of promoter regions in the Genomatix promoter database with similar size range as the binding regions identified by ChIP-chip (1000–1500 bp).

Sequencing:

Article Title: Summary of Recent Deal Activity
Article Snippet: Companies Type of deal Details Agilent Technologies, R&D agreement Ingenuity Systems and Agilent Technologies have signed an agreement to establish Ingenuity Systems integration between Agilent’s GeneSpring Analysis Platform and Ingenuity Pathways Analysis.. Genomics researchers will be able to easily exchange data between both applications, leveraging each system’s ability to analyze high-volume gene-expression data and to perform advanced biological pathway analysis.. The GeneSpring Analysis Platform integrates data and results from multiple measurement technologies, providing comprehensive statistical analysis, data mining and visualization tools.

Gene Expression:

Article Title: Regulatory networks: linking microarray data to systems biology.
Article Snippet: Gene regulation and aging are intrinsically linked and these links often reach directly to transcription factors and their actions in gene regulation.. However, it is very difficult to follow all the individual directions such factors can affect.. Therefore, the opposite approach became more popular recently, i.e. observing the endpoints of all these actions.



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<t>Microarray</t> analysis using mRNA from p16−/− BMDM compared to p16+/+ BMDM showed (A) decreased mRNA expression of classically activated macrophages-associated genes and (B) increased mRNA expression of alternatively activated macrophages-associated genes. Data is expressed as fold change relative to p16+/+ BMDM. (C) Differential gene expression in p16−/− BMDM relative to p16+/+ BMDM was correlated with the changes induced in IL-4-induced p16+/+ AAMφ. The figure shows 2log values of the probesets significantly (p<0.05) regulated only in p16−/− BMDM (red dots), only in IL-4-polarized p16+/+ AAMφ (green dots) and by both conditions (blue dots), compared to p16+/+ BMDM. The X-axis represents differences in gene expression induced by IL-4, whereas the Y-axis represents the effect of p16INKa-deficiency. These comparisons are depicted in the schematic representation of the protocol in the corresponding colors. Pearson Correlation analysis was done for probesets differentially expressed by both conditions (blue). (D) Heat map of p16+/+ BMDM, p16−/− BMDM, IL-4-polarized p16+/+ and p16−/− AAMφ gene expression profiles. Colors fluctuate from blue (poorly expressed) to green (intermediate expression) and yellow (high expression). Additional information regarding gene description, fold induction, and p-value can be found in Table S3.
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Image Search Results


Microarray analysis using mRNA from p16−/− BMDM compared to p16+/+ BMDM showed (A) decreased mRNA expression of classically activated macrophages-associated genes and (B) increased mRNA expression of alternatively activated macrophages-associated genes. Data is expressed as fold change relative to p16+/+ BMDM. (C) Differential gene expression in p16−/− BMDM relative to p16+/+ BMDM was correlated with the changes induced in IL-4-induced p16+/+ AAMφ. The figure shows 2log values of the probesets significantly (p<0.05) regulated only in p16−/− BMDM (red dots), only in IL-4-polarized p16+/+ AAMφ (green dots) and by both conditions (blue dots), compared to p16+/+ BMDM. The X-axis represents differences in gene expression induced by IL-4, whereas the Y-axis represents the effect of p16INKa-deficiency. These comparisons are depicted in the schematic representation of the protocol in the corresponding colors. Pearson Correlation analysis was done for probesets differentially expressed by both conditions (blue). (D) Heat map of p16+/+ BMDM, p16−/− BMDM, IL-4-polarized p16+/+ and p16−/− AAMφ gene expression profiles. Colors fluctuate from blue (poorly expressed) to green (intermediate expression) and yellow (high expression). Additional information regarding gene description, fold induction, and p-value can be found in Table S3.

Journal: Blood

Article Title: p16 INK4a deficiency promotes IL-4-induced polarization and inhibits proinflammatory signaling in macrophages

doi: 10.1182/blood-2010-10-313106

Figure Lengend Snippet: Microarray analysis using mRNA from p16−/− BMDM compared to p16+/+ BMDM showed (A) decreased mRNA expression of classically activated macrophages-associated genes and (B) increased mRNA expression of alternatively activated macrophages-associated genes. Data is expressed as fold change relative to p16+/+ BMDM. (C) Differential gene expression in p16−/− BMDM relative to p16+/+ BMDM was correlated with the changes induced in IL-4-induced p16+/+ AAMφ. The figure shows 2log values of the probesets significantly (p<0.05) regulated only in p16−/− BMDM (red dots), only in IL-4-polarized p16+/+ AAMφ (green dots) and by both conditions (blue dots), compared to p16+/+ BMDM. The X-axis represents differences in gene expression induced by IL-4, whereas the Y-axis represents the effect of p16INKa-deficiency. These comparisons are depicted in the schematic representation of the protocol in the corresponding colors. Pearson Correlation analysis was done for probesets differentially expressed by both conditions (blue). (D) Heat map of p16+/+ BMDM, p16−/− BMDM, IL-4-polarized p16+/+ and p16−/− AAMφ gene expression profiles. Colors fluctuate from blue (poorly expressed) to green (intermediate expression) and yellow (high expression). Additional information regarding gene description, fold induction, and p-value can be found in Table S3.

Article Snippet: We thank E. Vallez for mouse breeding, J. Brozek (Genfit SA, Loos, France) for microarray raw data analysis, T. Coevoet, N. Jouy and A. Lucas for technical assistance.

Techniques: Microarray, Expressing, Gene Expression

Representation of the relative microarray intensity values from a selection of down-regulated genes in p16+/+ and p16−/− BMDM with or without polarization (AAMφ) by 15 ng/mL IL-4 from day 0 of differentiation. Statistically significant differences are indicated (a: p<0.05 compared to p16+/+ BMDM; b: p<0.05 compared to p16−/− BMDM; c: p<0.05 compared to p16+/+ AAMφ.)

Journal: Blood

Article Title: p16 INK4a deficiency promotes IL-4-induced polarization and inhibits proinflammatory signaling in macrophages

doi: 10.1182/blood-2010-10-313106

Figure Lengend Snippet: Representation of the relative microarray intensity values from a selection of down-regulated genes in p16+/+ and p16−/− BMDM with or without polarization (AAMφ) by 15 ng/mL IL-4 from day 0 of differentiation. Statistically significant differences are indicated (a: p<0.05 compared to p16+/+ BMDM; b: p<0.05 compared to p16−/− BMDM; c: p<0.05 compared to p16+/+ AAMφ.)

Article Snippet: We thank E. Vallez for mouse breeding, J. Brozek (Genfit SA, Loos, France) for microarray raw data analysis, T. Coevoet, N. Jouy and A. Lucas for technical assistance.

Techniques: Microarray, Selection

Validation of  DNA   Microarray  Results by qPCR

Journal: Investigative Ophthalmology & Visual Science

Article Title: Perimysial Fibroblasts of Extraocular Muscle, as Unique as the Muscle Fibers

doi: 10.1167/iovs.08-2857

Figure Lengend Snippet: Validation of DNA Microarray Results by qPCR

Article Snippet: DNA Microarray Data Analysis Raw data from microarray scans were analyzed with microarray analysis software (GCOS 2.0; Affymetrix).

Techniques: Biomarker Discovery, Microarray