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Coexpression cluster:C4169

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Full id: C4169_Mast_CD14_large_migratory_Synoviocyte_immature_Mammary



Phase1 CAGE Peaks

Hg19::chr2:201676600..201676667,+p1@BZW1
Hg19::chr2:201676675..201676692,+p3@BZW1
Hg19::chr3:172144898..172144914,-p1@BZW1P1


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


GO IDGO nameFDR corrected p-value
GO:0006446regulation of translational initiation0.0351318733074296
GO:0006413translational initiation0.0351318733074296
GO:0003743translation initiation factor activity0.0351318733074296
GO:0022618protein-RNA complex assembly0.0351318733074296
GO:0006417regulation of translation0.0351318733074296
GO:0031326regulation of cellular biosynthetic process0.0351318733074296
GO:0008135translation factor activity, nucleic acid binding0.0351318733074296
GO:0009889regulation of biosynthetic process0.0351318733074296
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0354017033635543



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><br>


Cell Type
Ontology termp-valuen
animal cell2.89e-39679
eukaryotic cell2.89e-39679
native cell2.32e-30722
multi fate stem cell4.08e-28427
somatic stem cell5.06e-28433
somatic cell9.66e-28588
stem cell9.81e-28441
connective tissue cell1.72e-20361
mesenchymal cell4.71e-20354
motile cell2.16e-14386
classical monocyte1.86e-1242
CD14-positive, CD16-negative classical monocyte1.86e-1242
myeloid leukocyte7.74e-1272
defensive cell3.29e-1148
phagocyte3.29e-1148
leukocyte5.73e-10136
granulocyte monocyte progenitor cell1.46e-0967
macrophage dendritic cell progenitor2.52e-0961
myeloid lineage restricted progenitor cell5.86e-0966
fibroblast1.52e-0876
monopoietic cell1.59e-0859
monocyte1.59e-0859
monoblast1.59e-0859
promonocyte1.59e-0859
hematopoietic lineage restricted progenitor cell3.81e-07120
myeloid cell4.52e-07108
common myeloid progenitor4.52e-07108
stuff accumulating cell6.69e-0787
Uber Anatomy
Ontology termp-valuen
connective tissue6.91e-19371
musculoskeletal system1.04e-12167
skeletal system6.01e-11100
mesoderm7.86e-10315
mesoderm-derived structure7.86e-10315
presumptive mesoderm7.86e-10315
skeletal element9.58e-1090
bone marrow1.80e-0876
bone element9.05e-0882
immune system2.17e-0793


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)

{{{tfbs_overrepresentation_jaspar}}}



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
BCL3#602223.03140186915890.002464674760842910.0138562828953907
BRCA1#672213.45615376214920.007119807716084560.0296331884613301
ELK4#2005210.8237877723120.01091284719516480.0402048415484625
GTF2B#2959221.29588662288280.002878180589911410.0155853322253205
SIX5#147912211.3911435703060.009873820081429030.037083281627027
ZBTB33#10009221.10981668665410.002928597060603240.0156401998574525



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.