mirna expression patterns  (Broad Institute Inc)

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:

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

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

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:

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:

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

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

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

Journal: The Journal of surgical research

Article Title: MicroRNAs in Solid Tumors

doi: 10.1016/j.jss.2008.02.046

Figure Lengend Snippet: 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.

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:

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

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: Expressing

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

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.

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

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.

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: Biomarker Discovery, Expressing