NCBI GEO: archive for functional genomics data sets—update
Citations
10,584 citations
Cites methods from "NCBI GEO: archive for functional ge..."
...In the case of transcript data, STRING re-processes and maps the large number of experiments stored in the NCBI Gene Expression Omnibus (46), followed by normalization, redundancy reduction and Pearson correlation (described in (29))....
[...]
8,224 citations
Cites methods from "NCBI GEO: archive for functional ge..."
...As of March 2014, GEO consisted of more than 12 000 different platforms (GPL), 45 000 experiments (GSE) and over 1 million matrices (GSM)....
[...]
...The improvements can be attributed to the increased size of the GEO repository (experiments added since 2011) and to changes in our pipeline, namely: (i) the additional step to prune highly correlated samples using the Hobohm-2 algorithm and (ii) several minor improvements and bug fixes....
[...]
...The co-expression scores in STRING v10 are computed using a revised and improved pipeline (Figure 2), making use of all microarray gene expression experiments deposited in NCBI Gene Expression Omnibus (NCBI GEO) (37)....
[...]
6,201 citations
Cites methods from "NCBI GEO: archive for functional ge..."
...The new gene set libraries that were added include differentially expressed genes after drug, gene, disease and pathogen perturbations extracted from the national center for biotechnology information (NCBI) gene expression omnibus (GEO) through a crowdsourcing project....
[...]
...To extract gene sets from gene expression data deposited in the GEO (29), we established a crowdsourcing microtask project that asks participants to extract gene sets from GEO for the following categories: (1) single-gene perturbations in mammalian cells; (2) comparison of diseased versus normal tissues; (3) single-drug perturbations in mammalian cells; (4) perturbations applied to MCF7 cells; (5) comparison between young and old mammalian tissues; (6) endogenous ligand perturbations of mammalian cells; and (7) comparison of before and after pathogen infection of human cells....
[...]
...Participants of the microtasks were recruited via two Coursera massive online open courses (MOOCs) and worked voluntarily on finding relevant studies from the GEO database....
[...]
...Participants were also instructed to use the browser extension GEO2Enrichr (30) to extract differentially expressed gene sets from GEO....
[...]
...This peak is likely an artifact from submissions that arrive from the tool GEO2Enrichr, which has a default setting of posting the top 500 genes separated into up-regulated or down-regulated genes from signatures processed from GEO....
[...]
4,705 citations
Cites background from "NCBI GEO: archive for functional ge..."
...Large numbers of deep sequencing data sets are publicly available in databases such as the Gene Expression Omnibus (15) and the Short Read Archive (16), and these data sets allow us to assess post hoc the confidence in any given microRNA annotation....
[...]
...Large numbers of deep sequencing data sets are publicly available in databases such as the Gene Expression Omnibus (15) and the Short Read Archive (16), and these data sets allow us to assess post hoc the confidence in any given microRNA annotation....
[...]
3,597 citations
Cites methods from "NCBI GEO: archive for functional ge..."
...HITS-CLIP, PAR-CLIP, iCLIP and CLASH data were retrieved from the Gene Expression Omnibus (22), the supplementary data of original references or directly from authors on request (Supplementary Table S1)....
[...]
...Integration of Ago and other RBP binding sites from published CLIP data HITS-CLIP, PAR-CLIP, iCLIP and CLASH data were retrieved from the Gene Expression Omnibus (22), the supplementary data of original references or directly from authors on request (Supplementary Table S1)....
[...]
...In addition, we intend to integrate the cancer genomics data from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) into starBase to improve our understanding of miRNAmediated regulatory networks in developmental, physiological and pathological processes....
[...]
References
13,548 citations
12,142 citations
"NCBI GEO: archive for functional ge..." refers methods in this paper
...The GEO2R back end uses established Bioconductor (13) R packages to transform and analyse GEO data and presents results as a table of genes ordered by significance and that can be visualized with GEO Profile graphics....
[...]
11,864 citations
10,968 citations
"NCBI GEO: archive for functional ge..." refers background in this paper
...The Gene Expression Omnibus (GEO) repository (1) archives and freely distributes microarray, next-generation sequencing (NGS) and other forms of high-throughput functional genomic data....
[...]
8,106 citations