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Coexpression cluster:C1355: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159787117303009
|tf_chipseq_enrich=CEBPB#1051;4:5.31409841721654:0.00300804729391746:0.0159787117303009
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}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1355_Natural_NK_CD8_CD14_Eosinophils_Peripheral_spleen



Phase1 CAGE Peaks

Hg19::chr12:10425198..10425201,-p@chr12:10425198..10425201
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Hg19::chr12:10425221..10425239,-p@chr12:10425221..10425239
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Hg19::chr12:10425243..10425252,-p@chr12:10425243..10425252
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Hg19::chr12:10425255..10425266,-p@chr12:10425255..10425266
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Hg19::chr20:37493438..37493456,-p@chr20:37493438..37493456
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Hg19::chr2:85912270..85912280,+p12@GNLY


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
CD8-positive, alpha-beta T cell5.72e-4611
mature alpha-beta T cell3.34e-3518
alpha-beta T cell3.34e-3518
immature T cell3.34e-3518
mature T cell3.34e-3518
immature alpha-beta T cell3.34e-3518
natural killer cell4.21e-253
pro-NK cell4.21e-253
T cell5.41e-2525
pro-T cell5.41e-2525
lymphoid lineage restricted progenitor cell2.04e-2052
lymphocyte5.41e-2053
common lymphoid progenitor5.41e-2053
nucleate cell3.43e-1955
nongranular leukocyte3.77e-17115
leukocyte5.97e-16136
hematopoietic lineage restricted progenitor cell2.22e-12120
hematopoietic stem cell2.58e-12168
angioblastic mesenchymal cell2.58e-12168
single nucleate cell9.83e-123
mononuclear cell9.83e-123
hematopoietic cell1.59e-11177
hematopoietic oligopotent progenitor cell6.59e-10161
hematopoietic multipotent progenitor cell6.59e-10161
innate effector T cell8.68e-101
immature NK T cell8.68e-101
effector T cell8.68e-101
mature NK T cell8.68e-101
immature NK T cell stage IV8.68e-101
immature NK T cell stage I8.68e-101
immature NK T cell stage II8.68e-101
immature NK T cell stage III8.68e-101
Uber Anatomy
Ontology termp-valuen
epididymis4.87e-091
Disease
Ontology termp-valuen
pleomorphic carcinoma3.00e-091


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105145.314098417216540.003008047293917460.0159787117303009



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.