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Johns Hopkins HealthCare microarray for the mirnas

Microarray For The Mirnas, supplied by Johns Hopkins HealthCare, 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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1) Product Images from "Decreased AGO2 and DCR1 in PBMCs from War Veterans with PTSD leads to diminished miRNA resulting in elevated inflammation"

Article Title: Decreased AGO2 and DCR1 in PBMCs from War Veterans with PTSD leads to diminished miRNA resulting in elevated inflammation

Journal: Translational Psychiatry

doi: 10.1038/tp.2017.185

Figure Legend Snippet: miRNA expression profile in PBMCs from post-traumatic stress disorder (PTSD) patients. ( a ) Microarray analysis of miRNAs in PBMCs from normal human controls and PTSD patients. The heat map shows the expression intensities of all the miRNAs in each of the control and PTSD samples after microarray. ( b ) The volcano plot shows all the miRNAs with at least ±1.5 linear fold-difference. The green dots represents miRNAs significantly dysregulated in PTSD patients. (On y axis, 1.301 units is ~0.05). A total of 190 miRNAs were found to be significantly ( P- value<0.05) up- (7 miRNAs) or downregulated (183 miRNAs) by a linear fold-change value of ±1.5 or more ( c ). ( d ) The expression levels of the precursors of miRNAs as obtained from RNA-Seq analysis and presented here in the figure as fold-change values. The names represent the corresponding precursors of the miRNAs. These 35 miRNAs were further analyzed in the in vitro studies. PBMC, peripheral blood mononuclear cell.

Techniques Used: Expressing, Microarray, Control, RNA Sequencing, In Vitro

Argonaute 2 ( AGO2 ) and Dicer1 ( DCR1 ) transcript is lower in PBMCs of post-traumatic stress disorder (PTSD) patients and the abundance of mature miRNAs is reduced upon decreased expression of AGO2 and DCR1. ( a ) RNA-Seq analysis expression values of only the genes significantly dysregulated with log 2 fold-change of at least 1 or more (readers are requested to refer Bam et al. for the complete list of the genes), and different variants of AGO2 , DCR1 and STAT3 . The green dots indicate the position (expression values) of the different variants of AGO2 , DCR1 and STAT3 . The red dot is the position of DCR1 variant 5. ( b ) The FPKM values of the variants of AGO2 and DCR1 in control and PTSD samples after RNA-sequencing (RNA-Seq) analysis. The values above the bars indicate log 2 fold-change when compared between PTSD and controls. (FPKM: Fragments per kilobase of transcript per million mapped reads). ( c , d ) Quantitative real time PCR validation result of AGO2 and DCR1 transcripts in 22 controls and 18 PTSD PBMC RNA samples. The difference in expression level is provided as relative expression (RE) value by taking the controls as 1. In this assay, 18S rRNA was used as an internal control. ( e ) Linear fold-change values of 35 miRNAs, after microarray analysis, which were selected for further analysis by in vitro experiments. miRNA-451 was also included in the figure as a positive control because it was reported previously to be processed specifically through the AGO2-dependent pathway. ( f ) Relative expression levels of 34 miRNAs, listed in Figure 3a, after knockdown of AGO2 for 72 h by employing siRNA in THP-1 cells. The expression level is expressed relative to control which was taken as 1. PBMC, peripheral blood monnuclear cell.

Figure Legend Snippet: Argonaute 2 ( AGO2 ) and Dicer1 ( DCR1 ) transcript is lower in PBMCs of post-traumatic stress disorder (PTSD) patients and the abundance of mature miRNAs is reduced upon decreased expression of AGO2 and DCR1. ( a ) RNA-Seq analysis expression values of only the genes significantly dysregulated with log 2 fold-change of at least 1 or more (readers are requested to refer Bam et al. for the complete list of the genes), and different variants of AGO2 , DCR1 and STAT3 . The green dots indicate the position (expression values) of the different variants of AGO2 , DCR1 and STAT3 . The red dot is the position of DCR1 variant 5. ( b ) The FPKM values of the variants of AGO2 and DCR1 in control and PTSD samples after RNA-sequencing (RNA-Seq) analysis. The values above the bars indicate log 2 fold-change when compared between PTSD and controls. (FPKM: Fragments per kilobase of transcript per million mapped reads). ( c , d ) Quantitative real time PCR validation result of AGO2 and DCR1 transcripts in 22 controls and 18 PTSD PBMC RNA samples. The difference in expression level is provided as relative expression (RE) value by taking the controls as 1. In this assay, 18S rRNA was used as an internal control. ( e ) Linear fold-change values of 35 miRNAs, after microarray analysis, which were selected for further analysis by in vitro experiments. miRNA-451 was also included in the figure as a positive control because it was reported previously to be processed specifically through the AGO2-dependent pathway. ( f ) Relative expression levels of 34 miRNAs, listed in Figure 3a, after knockdown of AGO2 for 72 h by employing siRNA in THP-1 cells. The expression level is expressed relative to control which was taken as 1. PBMC, peripheral blood monnuclear cell.

Techniques Used: Expressing, RNA Sequencing, Variant Assay, Control, Real-time Polymerase Chain Reaction, Biomarker Discovery, Microarray, In Vitro, Positive Control, Knockdown

miRNAs downregulated in post-traumatic stress disorder (PTSD) target several pro-inflammatory genes. ( a ) Ingenuity Pathway Analysis (IPA) was performed with the dysregulated miRNAs in PTSD. The genes were included in the network and the miRNAs were connected by the IPA algorithm. The network shows direct interaction (predicted and proven) between miRNAs and target genes as indicated by solid arrows. ( b ) Principal component analysis (PCA) plot showing the relatedness of the samples. ( c ) IPA-generated network showing the interaction between miRNAs and targets after analyzing with the miRNAs obtained in the replicate samples. The red and blue colored target genes in the network correspond to up- and downregulated, respectively, validated for its expression level and reported either in the current manuscript or in our previous reports with studies on the same samples. For the miRNAs, the red color indicates upregulated and green indicates downregulated as per microarray analysis. ( d ) To validate the transcript levels of miRNA-targeted genes, qRT-PCR was performed to detect transcript of eight genes as shown in the graph (genes were selected based on the miRNA–gene interaction networks). The P- values of the genes under the curly brackets were <0.05.

Figure Legend Snippet: miRNAs downregulated in post-traumatic stress disorder (PTSD) target several pro-inflammatory genes. ( a ) Ingenuity Pathway Analysis (IPA) was performed with the dysregulated miRNAs in PTSD. The genes were included in the network and the miRNAs were connected by the IPA algorithm. The network shows direct interaction (predicted and proven) between miRNAs and target genes as indicated by solid arrows. ( b ) Principal component analysis (PCA) plot showing the relatedness of the samples. ( c ) IPA-generated network showing the interaction between miRNAs and targets after analyzing with the miRNAs obtained in the replicate samples. The red and blue colored target genes in the network correspond to up- and downregulated, respectively, validated for its expression level and reported either in the current manuscript or in our previous reports with studies on the same samples. For the miRNAs, the red color indicates upregulated and green indicates downregulated as per microarray analysis. ( d ) To validate the transcript levels of miRNA-targeted genes, qRT-PCR was performed to detect transcript of eight genes as shown in the graph (genes were selected based on the miRNA–gene interaction networks). The P- values of the genes under the curly brackets were <0.05.

Techniques Used: Generated, Expressing, Microarray, Quantitative RT-PCR

other:

Article Title: Dysregulated immune system networks in war veterans with PTSD is an outcome of altered miRNA expression and DNA methylation.
Article Snippet: Microarray for the miRNAs was performed by Johns Hopkins Memorial Institute (Deep Sequencing and Microarray Core Facility), Baltimore.

Article Title: Decreased AGO2 and DCR1 in PBMCs from War Veterans with PTSD leads to diminished miRNA resulting in elevated inflammation
Article Snippet: Microarray for the miRNAs was performed at Johns Hopkins Memorial Institute (Deep Sequencing and Microarray Core Facility, Baltimore, MD, USA).

Article Title: Plasma microRNAs are associated with domain-specific cognitive function in people with HIV
Article Snippet: AIDS 2021, 35:1795–1804 Keywords: cognition, cognitive function, HIV, microRNA opyright © 2021 Wolters Kluwer Health, Inc. All rights reserved. ersity, Glendale, Arizona, bDepartment of Applied Mathematics and Statistics, Johns Hopkins University, on of Biostatistics and Bioinformatics at The Sidney Kimmel Comprehensive Cancer Center, dDepartment of Hopkins University School of Medicine, Baltimore, eInstitute for Genome Sciences, University of Maryland, tment of Molecular and Comparative Pathobiology, gDivision of Clinical Pharmacology, Johns Hopkins of Medicine, Baltimore, Maryland, USA, hCumming School of Medicine, University of Calgary, iSouthern lgary, jDepartment of Medicine, kNeuroscience and Mental Health Institute, lDepartment of Psychiatry, rta, Edmonton, Alberta, Canada, mDepartment of Psychiatry and Behavioral Sciences, Johns Hopkins University e, and nDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, Leah H. Rubin, PhD, MPH, Department of Neurology, Johns Hopkins University School of Medicine, 600 N. r 6-113, Baltimore, MD.

Article Title: AhR Ligands Differentially Regulate miRNA-132 Which Targets HMGB1 and to Control the Differentiation of Tregs and Th-17 Cells During Delayed-Type Hypersensitivity Response
Article Snippet: Total RNAs including microRNAs were isolated using miRNeasy mini-kit and following the manufacturer's instructions (QIAGEN, Valencia, CA). miRNAs arrays were performed by Johns Hopkins sequencing core facility, Baltimore.

Microarray:

Article Title: MicroRNA deregulation in polycythemia vera and essential thrombocythemia patients
Article Snippet: .. We thank Hai Xu from Johns Hopkins University for his assistance in microRNA microarray experiments. .. We thank Drs. Azra Raza and Naomi Galili from Columbia University Medical Center, Drs. Erik Langhoff, Mary Sano, and Elisa Sanchez-Valencia from James J. Peters VA Medical Center, and Dr. Robert Brodsky from Johns Hopkins University for their continuing support throughout this work.

Article Title: Fatty acid amide hydrolase (FAAH) blockade ameliorates experimental colitis by altering microRNA expression and suppressing inflammation
Article Snippet: Readings were measured using a Luminex System (Austin, TX) and calculated using BioRad software (Bio-Plex manager 6.1). .. Samples were stored at −80° C until they were sent to the Johns Hopkins University sequencing core facility for miRNAs microarray analysis. .. 2.7 miRNAs isolation and microarray analysis Cells from MLNs and PPs were immediately placed in TRIzol reagent from a miRNeasy mini-kit (QIAGEN, Valencia, CA).

Expressing:

Article Title: Clinical Application of MicroRNA Testing in Neuroendocrine Tumors of the Gastrointestinal Tract
Article Snippet: .. Matthaei and colleagues from Johns Hopkins Hospital identified a miRNAs expression pattern including nine miRNAs (miR-24, miR-30a-3p, miR-18a, miR-92a, miR-342-3p, miR-99b, miR-106b, miR-142-3p, and miR-532-3p) derived from the analysis of selected miRNAs in cyst fluid samples, which successfully discriminated cystic forms of PanNETs from other pancreatic cystic lesions, such as intraductal papillary mucinous neoplasms (IPMN) [51]. .. Another group from the Johns Hopkins investigated cell-free circulating miRNA profiles on a relatively large series of patients with pancreatic adenocarcinoma, healthy controls, subjects with chronic pancreatitis, and PanNETs [52].

Article Title: Clinical Application of MicroRNA Testing in Neuroendocrine Tumors of the Gastrointestinal Tract
Article Snippet: .. Matthaei and colleagues from Johns Hopkins Hospital identified a miRNAs expression pattern including nine miRNAs (miR-24, miR-30a-3p, miR-18a, miR-92a, miR-342-3p, miR-99b, miR-106b, miR-142-3p, and miR-532-3p) derived from the analysis of selected miRNAs in cyst fluid samples, which successfully discriminated cystic forms of PanNETs from other pancreatic cystic lesions, such as intraductal papillary mucinous neoplasms (IPMN) [ ]. .. Another group from the Johns Hopkins investigated cell-free circulating miRNA profiles on a relatively large series of patients with pancreatic adenocarcinoma, healthy controls, subjects with chronic pancreatitis, and PanNETs [ ].

Derivative Assay:

Article Title: Clinical Application of MicroRNA Testing in Neuroendocrine Tumors of the Gastrointestinal Tract
Article Snippet: .. Matthaei and colleagues from Johns Hopkins Hospital identified a miRNAs expression pattern including nine miRNAs (miR-24, miR-30a-3p, miR-18a, miR-92a, miR-342-3p, miR-99b, miR-106b, miR-142-3p, and miR-532-3p) derived from the analysis of selected miRNAs in cyst fluid samples, which successfully discriminated cystic forms of PanNETs from other pancreatic cystic lesions, such as intraductal papillary mucinous neoplasms (IPMN) [ ]. .. Another group from the Johns Hopkins investigated cell-free circulating miRNA profiles on a relatively large series of patients with pancreatic adenocarcinoma, healthy controls, subjects with chronic pancreatitis, and PanNETs [ ].

Sequencing:

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Length distribution of known, novel and total miRNAs in all 9 libraries. X -axis represents the base numbers of miRNAs; Y -axis represents the accumulation numbers with the same length.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: Length distribution of known, novel and total miRNAs in all 9 libraries. X -axis represents the base numbers of miRNAs; Y -axis represents the accumulation numbers with the same length.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques:

The stem-loop structure of six novel miRNA precursors with most abundant expression. Mature miRNA sequences are signed in red and miRNA* are marked in purple.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: The stem-loop structure of six novel miRNA precursors with most abundant expression. Mature miRNA sequences are signed in red and miRNA* are marked in purple.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques: Expressing

Differentially expressed miRNAs in salt and alkali stress during the germination of R108. Fold change values greater than 1.5 or less than 0.67 indicate upregulated or downregulated miRNAs. ( A – C ) The Venn diagram of the common and specific miRNAs differentially expressed miRNAs in salt stress and alkali stress. A , total differently expressed miRNAs; B , down-regulated miRNAs only; C , up-regulated miRNAs; ( D , E ) The expression patterns and hierarchal clustering of differentially expressed known miRNAs in salt and alkali stress, respectively; ( F , G ) The expression patterns and hierarchal clustering of differentially expressed putative miRNAs in salt and alkali stress.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: Differentially expressed miRNAs in salt and alkali stress during the germination of R108. Fold change values greater than 1.5 or less than 0.67 indicate upregulated or downregulated miRNAs. ( A – C ) The Venn diagram of the common and specific miRNAs differentially expressed miRNAs in salt stress and alkali stress. A , total differently expressed miRNAs; B , down-regulated miRNAs only; C , up-regulated miRNAs; ( D , E ) The expression patterns and hierarchal clustering of differentially expressed known miRNAs in salt and alkali stress, respectively; ( F , G ) The expression patterns and hierarchal clustering of differentially expressed putative miRNAs in salt and alkali stress.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques: Expressing

Gene ontology classification of potential target genes for differentially expressed miRNAs in salt ( A ) and alkali ( B ) stress. Red, green and blue represent three GO ontologies: biological progress, cellular component and molecular function, respectively.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: Gene ontology classification of potential target genes for differentially expressed miRNAs in salt ( A ) and alkali ( B ) stress. Red, green and blue represent three GO ontologies: biological progress, cellular component and molecular function, respectively.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques:

The bubble graph of salt/alkali response miRNA targets analysis in the KEGG (kyoto encyclopedia of genes and genomes). ( A ) Top 17 pathways enriched by miRNA responsive targets in salt stress; ( B ) Top 15 pathways enriched by miRNA responsive targets in alkali stress.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: The bubble graph of salt/alkali response miRNA targets analysis in the KEGG (kyoto encyclopedia of genes and genomes). ( A ) Top 17 pathways enriched by miRNA responsive targets in salt stress; ( B ) Top 15 pathways enriched by miRNA responsive targets in alkali stress.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques:

Validation of 11 miRNAs expressions in M. truncatula using RT-qPCR. ( A – K ) Expressional abundance of each miRNA gene in the control sample was set as 1 and fold changes of each miRNA gene relative to the control sample were calculated. The red plots are small RNA sequencing results and green represents the RT-qPCR results.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: Validation of 11 miRNAs expressions in M. truncatula using RT-qPCR. ( A – K ) Expressional abundance of each miRNA gene in the control sample was set as 1 and fold changes of each miRNA gene relative to the control sample were calculated. The red plots are small RNA sequencing results and green represents the RT-qPCR results.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques: Biomarker Discovery, Quantitative RT-PCR, Control, RNA Sequencing

The expressions of 4 miRNA putative targets in R108 after treated with salt and alkali stress. The target genes expression identified with RT-qPCR in the left versus the sRNA-SEQ results of corresponding miRNAs in the right, ( A ) miR319-MYB; ( B , C ) miR395-ATPS and –Bhlh130; ( D ) miR408-BBLP. *: p < 0.05, **: p < 0.01.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: The expressions of 4 miRNA putative targets in R108 after treated with salt and alkali stress. The target genes expression identified with RT-qPCR in the left versus the sRNA-SEQ results of corresponding miRNAs in the right, ( A ) miR319-MYB; ( B , C ) miR395-ATPS and –Bhlh130; ( D ) miR408-BBLP. *: p < 0.05, **: p < 0.01.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques: Expressing, Quantitative RT-PCR

Diagrammatic representation of the cleavage sites of two miRNA targets. The CDS (coding sequence) of target gene is represented by black boxes and the cracks are the complementary site of miRNA. Black arrows indicate the exact cleavage site of mRNA.

Journal: International Journal of Molecular Sciences

Article Title: Genome-Wide Identification of microRNAs in Response to Salt/Alkali Stress in Medicago truncatula through High-Throughput Sequencing

doi: 10.3390/ijms19124076

Figure Lengend Snippet: Diagrammatic representation of the cleavage sites of two miRNA targets. The CDS (coding sequence) of target gene is represented by black boxes and the cracks are the complementary site of miRNA. Black arrows indicate the exact cleavage site of mRNA.

Article Snippet: This study was aimed to identify novel miRNAs and the miRNA expression patterns in the leguminous model plant R108 ( Medicago truncatula ).

Techniques: Sequencing

MiRNA processing. Reprinted with permission from Macmillan Publishers Ltd.: Nature Reviews Cancer, Oncomirs-microRNAs with a role in cancer. 2006;6:259–269, Copyright 2006.

Journal: The Journal of surgical research

Article Title: MicroRNAs in Solid Tumors

doi: 10.1016/j.jss.2008.02.046

Article Snippet: They also found that protein coding tumor suppressor genes and oncogenes were the targets for the differentially expressed miRNAs [ 34 ]. table ft1 table-wrap mode="anchored" t5 caption a7 Year Author Tumor type No. of samples Significant findings 2005 He et al. [ 43 ] PTC 20T, 20N (matched) miRNA expression pattern (17 over-expressed, 6 underexpressed) 2005 Iorio et al. [ 40 ] Breast 76T, 9N miRNA expression pattern, let-7 underexpression correlated with lymph node metastasis and higher proliferation index 2006 Pallante et al. [ 42 ] PTC 30T, 10N 5 miRNA overexpressed, miR-21 described in carcinogenesis 2006 Roldo et al. [ 39 ] PET 44T, 12N miRNA expression pattern, miR-21 correlation with stage and proliferation index 2006 Yanaihara et al. [ 35 ] Lung 104T, 104N (matched) miRNA expression pattern (43 underexpressed), miR-155 and let-7-a2 associated with poorer survival 2006 Volinia et al. [ 34 ] Mixed 363T, 177N Tumor-specific miRNA expression patterns, oncogenic target genes described 2006 Bandres et al. [ 31 ] CRC 12T, 12N (matched) miRNA expression pattern, miR-31 correlation with stage 2006 Murakami et al. [ 41 ] HCC 25T, 25N (matched) miRNA expression pattern, correlation with tumor grade 2007 Lee et al. [ 36 ] PDA 28T, 15N (matched) miRNA expression pattern 2007 Bloomston et al. [ 37 ] PDA 65T, 65N (matched) miRNA expression pattern (21 overexpressed), miR-196a2 associated with poorer survival 2007 Iorio et al. [ 28 ] Ovarian 69T, 15N miRNA expression pattern, correlation with pathologic features 2008 Schetter et al. [ 33 ] CRC 84T, 84N (matched-US) 113T, 113N (matched-Chinese) miRNA expression pattern in US samples and verified in Chinese samples, miR-21 correlated with TNM stage Open in a separate window PTC = papillary thyroid cancer; PET = pancreatic endocrine tumor; CRC = colorectal cancer; HCC = hepatocellular carcinoma; PDA = pancreatic ductal adenocarcinoma; T = tumor; N = normal; “matched” refers to adjacent benign tissue; TNM = tumor-node-metastasis. caption a8 Overview of miRNA Studies in Solid Tumors Microarray analysis has been invaluable in evaluating lung cancers.

Techniques:

Overview of miRNA Studies in Solid Tumors

Journal: The Journal of surgical research

Article Title: MicroRNAs in Solid Tumors

doi: 10.1016/j.jss.2008.02.046

Figure Lengend Snippet: Overview of miRNA Studies in Solid Tumors

Techniques: Expressing

Marginal correlations of m- and miRNA expression levels are typically and inappropriately positive in all datasets under analysis. Further, in the Madison and Broad datasets the amount of variation in targeted mRNA expression captured by that of targeting miRNA is extremely low. In the combined dataset, high R 2 values are indicative only of the amount of variation in mRNA expression due to data origin.

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Marginal correlations of m- and miRNA expression levels are typically and inappropriately positive in all datasets under analysis. Further, in the Madison and Broad datasets the amount of variation in targeted mRNA expression captured by that of targeting miRNA is extremely low. In the combined dataset, high R 2 values are indicative only of the amount of variation in mRNA expression due to data origin.

Article Snippet: The second data source was derived from that produced from a study of miRNA expression patterns over a wide variety of tumor and normal tissue types conducted by the Broad Institute .

Techniques: Expressing

Improvements in the percentages of variation in targeted mRNA expression are observed through use of the adjusted R 2 statistic. Partial correlations of proxies to targeting Ago 2 RISCs and targeted mRNAs are lower than those of m/miRNA expressions. Paired Wilcoxon tests of the hypothesis H 0 : μ 0 −μ 1 = 0 vs. H A : μ 0 −μ 1 ≠0 were rejected for the Madison ( p = 0.0135), Broad ( p = 0.0186) and combined ( p <0.0001) datasets, where μ 0 and μ 1 refer to mean correlations of marginal m/miRNA expression and mean partial correlations respectively.

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Improvements in the percentages of variation in targeted mRNA expression are observed through use of the adjusted R 2 statistic. Partial correlations of proxies to targeting Ago 2 RISCs and targeted mRNAs are lower than those of m/miRNA expressions. Paired Wilcoxon tests of the hypothesis H 0 : μ 0 −μ 1 = 0 vs. H A : μ 0 −μ 1 ≠0 were rejected for the Madison ( p = 0.0135), Broad ( p = 0.0186) and combined ( p <0.0001) datasets, where μ 0 and μ 1 refer to mean correlations of marginal m/miRNA expression and mean partial correlations respectively.

Techniques: Expressing

Hash marks denote the 95% confidence level of identification numbers under the no-targeting null for the miRNA and validation technique under consideration. Overall, 7.83% of computational predicted targets were verified using marginal expression level comparisons, and 4 miRNAs showed substantially larger numbers of verifications than what would be typically expected. After compensating for biological and idiosyncratic effects, 25.68% of these targets were verified, and 9 miRNAs showed large numbers of identifications.

Journal: PLoS Computational Biology

Article Title: Statistical Use of Argonaute Expression and RISC Assembly in microRNA Target Identification

doi: 10.1371/journal.pcbi.1000516

Figure Lengend Snippet: Hash marks denote the 95% confidence level of identification numbers under the no-targeting null for the miRNA and validation technique under consideration. Overall, 7.83% of computational predicted targets were verified using marginal expression level comparisons, and 4 miRNAs showed substantially larger numbers of verifications than what would be typically expected. After compensating for biological and idiosyncratic effects, 25.68% of these targets were verified, and 9 miRNAs showed large numbers of identifications.

Techniques: Biomarker Discovery, Expressing

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microarray for the mirnas (Johns Hopkins HealthCare)

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1) Product Images from "Decreased AGO2 and DCR1 in PBMCs from War Veterans with PTSD leads to diminished miRNA resulting in elevated inflammation"

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