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Coexpression cluster:C4241

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Full id: C4241_mature_Hepatocyte_iPS_H9_HES3GFP_Olfactory_liver



Phase1 CAGE Peaks

Hg19::chr2:64068986..64068997,+p6@UGP2
Hg19::chr2:64069016..64069039,+p1@UGP2
Hg19::chr2:64069042..64069056,+p5@UGP2


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>


Cell Type
Ontology termp-valuen
fibroblast4.08e-1076
skin fibroblast1.23e-0823
fat cell1.82e-0815
muscle precursor cell4.87e-0758
myoblast4.87e-0758
multi-potent skeletal muscle stem cell4.87e-0758
electrically responsive cell5.88e-0761
electrically active cell5.88e-0761
Uber Anatomy
Ontology termp-valuen
surface structure4.56e-1299
dense mesenchyme tissue1.45e-1073
somite2.43e-1071
presomitic mesoderm2.43e-1071
presumptive segmental plate2.43e-1071
dermomyotome2.43e-1071
trunk paraxial mesoderm2.43e-1071
paraxial mesoderm2.98e-1072
presumptive paraxial mesoderm2.98e-1072
multilaminar epithelium1.50e-0983
integument7.97e-0946
integumental system7.97e-0946
skeletal muscle tissue2.91e-0862
striated muscle tissue2.91e-0862
myotome2.91e-0862
mesenchyme3.06e-08160
entire embryonic mesenchyme3.06e-08160
muscle tissue3.07e-0864
musculature3.07e-0864
musculature of body3.07e-0864
trunk mesenchyme7.60e-08122
skin of body1.15e-0741
epithelial vesicle2.23e-0778


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#90536.336201576962630.003930750035764890.0190533557498027
CTCF#1066435.360256373075030.0064925092527670.0280287356915399
E2F1#186934.907389214879320.008460985347239390.0326397831300681
E2F6#187635.017155731697390.00791769806886330.032322888973694
EGR1#195834.988179094810140.008056488137383440.0321542175397504
ELF1#199734.258097958807540.01295179875054610.0463641100157081
HDAC2#3066313.41562023662630.0004140761399857210.0039232239847563
HMGN3#932438.178547723350590.001827766942164210.0108930696001306
NFKB1#479035.488063424193840.006049381815655430.0270204168781643
RAD21#5885310.35503389545630.0009004912073565420.00665909517844012
RDBP#79363153.6384039900252.75057764221434e-071.40130526036695e-05
SIN3A#2594235.408884726815140.006318961977991520.0277579840176428
STAT3#6774310.51946499715420.0008589184530415310.00644013097258988
TAF7#6879311.43306940492390.0006690181981945830.00544468102557812
YY1#752834.911170749853860.008441455341808260.033024316543419
ZBTB7A#5134137.35190930787590.002516255860282270.0140554765894004



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.