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Coexpression cluster:C3737

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Full id: C3737_chronic_Hodgkin_acute_merkel_Hep2_hereditary_cord



Phase1 CAGE Peaks

Hg19::chr18:657610..657633,+p2@TYMS
Hg19::chr18:657637..657729,+p1@TYMS
Hg19::chr18:657733..657742,+p4@TYMS


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
epithelial cell7.67e-15254
animal cell9.47e-15679
eukaryotic cell9.47e-15679
embryonic cell2.19e-10248
non-terminally differentiated cell9.68e-09180
native cell2.15e-08722
migratory neural crest cell2.12e-0741
neurectodermal cell5.76e-0759
Uber Anatomy
Ontology termp-valuen
larynx3.53e-079
Disease
Ontology termp-valuen
cancer2.07e-32235
disease of cellular proliferation2.01e-31239
hematologic cancer1.15e-2051
immune system cancer1.15e-2051
organ system cancer6.64e-18137
leukemia1.29e-1739
myeloid leukemia8.99e-1431
cell type cancer1.46e-13143
carcinoma7.65e-11106


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
CCNT2#90536.336201576962630.003930750035764890.0189934118157328
CTCF#1066435.360256373075030.0064925092527670.0279317504469325
E2F1#186934.907389214879320.008460985347239390.0325172713405827
E2F4#1874312.66806031528440.0004917987006298980.00436871348941788
E2F6#187635.017155731697390.00791769806886330.032203305109978
ELF1#199734.258097958807540.01295179875054610.0462073139888052
GABPB1#255337.067683836182170.002832212825417420.0154043055553468
MAX#414936.452555509007120.003721913834265510.0186406252787059
MYC#460935.22228187160940.007020843755740150.0294347838708099
NFKB1#479035.488063424193840.006049381815655430.0269501082389301
NRF1#4899312.21027944771090.0005492172401020010.00471010833790548
SIN3A#2594235.408884726815140.006318961977991520.0276556204173598
TFAP2C#7022310.80922860986020.0007916746575753130.00615786918615537
YY1#752834.911170749853860.008441455341808260.0329219595370668



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.