Personal tools

Coexpression cluster:C3061

From FANTOM5_SSTAR

Revision as of 14:46, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3061_granulocyte_testicular_hepatoblastoma_HES3GFP_retinoblastoma_H9_Hodgkin



Phase1 CAGE Peaks

Hg19::chr10:96305516..96305531,+p2@HELLS
Hg19::chr10:96305535..96305598,+p1@HELLS
Hg19::chr10:96305610..96305620,+p3@HELLS


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><br>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell5.81e-09253
Disease
Ontology termp-valuen
cancer1.04e-53235
disease of cellular proliferation2.49e-51239
cell type cancer2.97e-34143
carcinoma8.01e-28106
organ system cancer4.19e-24137
hematologic cancer2.36e-1451
immune system cancer2.36e-1451
leukemia6.53e-1139
germ cell and embryonal cancer1.45e-0722
germ cell cancer1.45e-0722
myeloid leukemia2.09e-0731


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
BRCA1#672320.18423064322380.0001215704860271640.00163912987221675
CEBPB#105137.971147625824820.001974187055288560.0114903099569372
CHD2#1106310.34402283411690.0009033701102746880.00658296615594322
CTCFL#140690319.74647435897440.0001298372005551160.00171018632725133
E2F1#186934.907389214879320.008460985347239390.0323517920729419
E2F4#1874312.66806031528440.0004917987006298980.00435316251335588
E2F6#187635.017155731697390.00791769806886330.0320336433181225
ELF1#199734.258097958807540.01295179875054610.0459998949094839
ETS1#211339.728760922202340.001085840092584840.00759775247417042
JUND#372736.994663941871030.002921845042734990.0156137215727691
KAT2A#26483616.094.23369446870294e-093.45980294692384e-07
MAX#414936.452555509007120.003721913834265510.0185684990416
MXI1#460139.96157162875930.001011470541259020.00718032707032021
NFKB1#479035.488063424193840.006049381815655430.0268538864897878
PAX5#507936.669565531177830.003370290999677260.0172240077175227
SIN3A#2594235.408884726815140.006318961977991520.0275356143872598
SMARCB1#6598212.16847718743830.008675002221921740.0329685439778496
SP1#666735.69838137814090.005403962701712170.0245405887731158
TAF7#6879311.43306940492390.0006690181981945830.00540467138004672
YY1#752834.911170749853860.008441455341808260.0327860600387919
ZBTB33#10009331.66472502998123.14815888737575e-050.000633019957717821
ZEB1#6935316.88843201754390.0002075486917327580.00241867639097049



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.