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Coexpression cluster:C4712

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Full id: C4712_Mast_clear_cord_immature_lung_Reticulocytes_CD8



Phase1 CAGE Peaks

Hg19::chr8:101322132..101322152,-p3@RNF19A
Hg19::chr8:101322154..101322207,-p1@RNF19A
Hg19::chr8:101322279..101322300,-p4@RNF19A


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
adult organism4.58e-19115
hematopoietic system2.72e-15102
blood island2.72e-15102
hemolymphoid system5.22e-15112
neural tube1.87e-1357
neural rod1.87e-1357
future spinal cord1.87e-1357
neural keel1.87e-1357
anterior neural tube1.83e-1242
regional part of forebrain3.33e-1241
forebrain3.33e-1241
future forebrain3.33e-1241
gray matter5.53e-1234
brain grey matter5.53e-1234
telencephalon6.27e-1234
regional part of telencephalon7.78e-1233
cerebral hemisphere4.05e-1132
bone marrow4.12e-1180
central nervous system9.78e-1182
immune system1.16e-10115
bone element8.00e-1086
regional part of brain1.33e-0959
cerebral cortex6.82e-0925
pallium6.82e-0925
brain1.76e-0869
future brain1.76e-0869
regional part of cerebral cortex2.28e-0822
skeletal element7.48e-08101
skeletal system7.48e-08101
neocortex2.29e-0720
regional part of nervous system6.77e-0794
nervous system6.77e-0794


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#90536.336201576962630.003930750035764890.0191190202582549
CTCF#1066435.360256373075030.0064925092527670.0281357333547607
E2F1#186934.907389214879320.008460985347239390.032780236995227
E2F6#187635.017155731697390.00791769806886330.0324395460599433
EGR1#195834.988179094810140.008056488137383440.0322552926696385
ELF1#199734.258097958807540.01295179875054610.0465043802973247
ESR1#2099330.76860329615453.43136389821584e-050.000679242255810773
ETS1#211339.728760922202340.001085840092584840.00765416127358718
HMGN3#932438.178547723350590.001827766942164210.0109242389649015
IRF1#365937.63716375356390.002244692747297240.0128753001886521
MYC#460935.22228187160940.007020843755740150.0296119013409961
NFKB1#479035.488063424193840.006049381815655430.0270864474788955
NRF1#4899312.21027944771090.0005492172401020010.00473538341773408
PAX5#507936.669565531177830.003370290999677260.0173693472349022
POU2F2#545239.106124057742520.001324165192682130.00885821730454323
RAD21#5885310.35503389545630.0009004912073565420.00668798188060801
REST#597839.650028716128020.001112636247114590.00771546491019193
SIN3A#2594235.408884726815140.006318961977991520.0278329075121023
SP1#666735.69838137814090.005403962701712170.0247917619417578
STAT3#6774310.51946499715420.0008589184530415310.00645635413251795
USF1#739136.361499277207960.00388404057290560.0191224868426761
YY1#752834.911170749853860.008441455341808260.0331310467659945
ZBTB7A#5134137.35190930787590.002516255860282270.0140946766313767
ZNF263#1012738.221841637010680.001799043925565870.01101608516312



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.