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Coexpression cluster:C1760

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Full id: C1760_brain_occipital_temporal_duodenum_parietal_medulloblastoma_myeloma



Phase1 CAGE Peaks

Hg19::chr16:28303874..28303916,+p2@SBK1
Hg19::chr1:200992739..200992763,-p3@KIF21B
Hg19::chr1:200992771..200992815,-p1@KIF21B
Hg19::chr1:200992827..200992867,-p2@KIF21B
Hg19::chr3:111393542..111393579,+p1@PLCXD2


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>


Uber Anatomy
Ontology termp-valuen
central nervous system1.05e-1982
neural tube6.24e-1957
neural rod6.24e-1957
future spinal cord6.24e-1957
neural keel6.24e-1957
regional part of nervous system5.14e-1894
nervous system5.14e-1894
adult organism2.28e-16115
regional part of forebrain3.53e-1641
forebrain3.53e-1641
future forebrain3.53e-1641
anterior neural tube1.03e-1542
brain3.94e-1569
future brain3.94e-1569
regional part of brain9.86e-1559
telencephalon1.17e-1434
gray matter1.43e-1434
brain grey matter1.43e-1434
cerebral hemisphere3.31e-1432
regional part of telencephalon4.12e-1433
regional part of cerebral cortex1.94e-1322
neocortex1.73e-1220
cerebral cortex1.68e-1125
pallium1.68e-1125
neural plate1.38e-1086
presumptive neural plate1.38e-1086
neurectoderm1.86e-1090
pre-chordal neural plate2.82e-1061
blood5.44e-0915
haemolymphatic fluid5.44e-0915
organism substance5.44e-0915
hematopoietic system6.39e-07102
blood island6.39e-07102
Disease
Ontology termp-valuen
hematologic cancer1.16e-0851
immune system cancer1.16e-0851


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
E2F1#186954.907389214879320.0003512818099256460.00352696798181355
E2F6#187644.013724585357910.006632118233933880.0282934437414248
EGR1#195854.988179094810140.0003237398000590710.00330702865594379
ETS1#211335.83725655332140.009253279045631430.0349715281988384
MYC#460944.177825497287520.005691969036823440.0256787712413306
SIN3A#2594244.327107781452110.004977052855762880.0232436803292501
SRF#672238.278306957300690.003404846073776150.0173606756382906



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.