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Coexpression cluster:C1983

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Full id: C1983_gastric_CD14_squamous_amniotic_myeloma_Placental_Wilms



Phase1 CAGE Peaks

Hg19::chr7:115850556..115850626,+p1@TES
Hg19::chr7:115850628..115850647,+p2@TES
Hg19::chr7:115850662..115850674,+p3@TES
Hg19::chr7:115897949..115897975,+p5@TES
Hg19::chr7:115898149..115898224,+p4@TES


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><br>


Uber Anatomy
Ontology termp-valuen
hematopoietic system2.09e-1198
blood island2.09e-1198
hemolymphoid system1.92e-10108
bone marrow8.28e-0976
immune system2.51e-0893
skeletal element2.41e-0790
lateral plate mesoderm4.36e-07203
mesoderm4.79e-07315
mesoderm-derived structure4.79e-07315
presumptive mesoderm4.79e-07315


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
CHD2#110636.206413700470110.007774550126275590.0319596253104816
E2F4#187437.600836189170660.004354147360375710.0206513531412479
ELK4#200539.741408995080820.00212558656574340.0122879516959856
ESR1#2099318.46116197769270.000326633459097560.00333072367063953
FOS#235335.398773185336640.01153895317278740.0421959639500262
GTF2F1#296237.643796526054590.00428415496412050.0203480313019137
NANOG#79923317.54686708860760.0003794200090681830.0037617473255242
NFYA#4800311.05534841989830.001470892907644430.00941405713822014
NFYB#4801310.05587595212190.001938165606725460.011389190221167
RFX5#599337.228746496317060.00502918278958660.0234692949670078
SP2#6668315.69211829630680.0005272235913302770.00456421623466038
TCF7L2#693436.462105937882410.006930108755689190.0293239457230136
ZEB1#6935310.13305921052630.001895556924357070.0111651948351998



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.