Personal tools

Coexpression cluster:C986

From FANTOM5_SSTAR

Revision as of 16:56, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C986_cerebellum_CD4_granulocyte_Mast_pineal_non_pituitary



Phase1 CAGE Peaks

Hg19::chr11:107328527..107328569,-p1@CWF19L2
Hg19::chr13:107220455..107220517,-p1@ARGLU1
Hg19::chr1:155826967..155827018,-p1@GON4L
Hg19::chr1:53018743..53018777,-p1@ZCCHC11
Hg19::chr4:68411245..68411267,-p3@CENPC1
Hg19::chr5:70751463..70751503,+p1@BDP1
Hg19::chr6:99873145..99873196,-p1@PNISR
Hg19::chrX:77041685..77041716,-p1@ATRX


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

GO IDGO nameFDR corrected p-value
GO:0003676nucleic acid binding0.0204835785567552
GO:0003677DNA binding0.0228631337756485
GO:0005720nuclear heterochromatin0.0330563092809218
GO:0044427chromosomal part0.0330563092809218
GO:0005694chromosome0.0330563092809218
GO:0000792heterochromatin0.0330563092809218
GO:0000790nuclear chromatin0.0330563092809218
GO:0006306DNA methylation0.0330563092809218
GO:0006305DNA alkylation0.0330563092809218
GO:0006304DNA modification0.0333998818179596
GO:0005634nucleus0.0333998818179596
GO:0000776kinetochore0.0333998818179596
GO:0043414biopolymer methylation0.0447173103598427
GO:0003678DNA helicase activity0.0452035226043505



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 organism5.32e-25114
neural tube7.34e-1756
neural rod7.34e-1756
future spinal cord7.34e-1756
neural keel7.34e-1756
regional part of nervous system1.27e-1553
regional part of brain1.27e-1553
nervous system1.43e-1589
regional part of forebrain5.55e-1541
forebrain5.55e-1541
anterior neural tube5.55e-1541
future forebrain5.55e-1541
central nervous system1.03e-1481
brain6.76e-1368
future brain6.76e-1368
brain grey matter3.14e-1234
gray matter3.14e-1234
telencephalon1.32e-1134
regional part of telencephalon2.00e-1132
cerebral hemisphere4.56e-1132
neurectoderm2.56e-1086
neural plate9.58e-1082
presumptive neural plate9.58e-1082
regional part of cerebral cortex1.09e-0822
cerebral cortex2.03e-0825
pallium2.03e-0825
neocortex8.34e-0820
pre-chordal neural plate9.27e-0861


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
ATF3#46738.423690447253280.004171166389609930.0198719298679168
E2F1#186963.680541911159490.001366491550819140.00899388776632215
ELF1#199784.258097958807549.24826870984006e-060.000246712627276369
FOXA1#316956.925887343365910.0002650891078941710.00283838849080986
FOXA2#317039.236423907249470.003211939548395410.016844175470493
GABPB1#255354.417302397613860.002182228654850360.0125882230590399
HEY1#2346284.040111043105711.4081650274634e-050.000339490644744346
IRF1#365954.773227345977440.001525548480294670.0097150462032619
MXI1#460144.980785814379650.005094415320429170.0236974720136425
MYC#460953.263926169755880.008583639497943430.0327046341076836
NFKB1#479064.116047568145380.0007299856589784310.00581754843479957
POLR2A#543082.147453176558070.002210725788971910.0127308111311445
POU2F2#545255.691327536089080.000670954773528490.00541612657230963
RFX5#599346.023955413597550.00252649680619860.0139921942911536
SIN3A#2594264.056663545111350.000792208907523070.00612870415502236
SIX5#14791248.54335767772950.000677999305962630.00547003240752654
SP1#666753.561488361338060.005813761866596070.0261356523581882
SRF#672246.89858913108390.001522071904568780.00970118806549854
TAF1#687283.343046285745296.40776711117462e-050.00104451504498824
TAF7#687968.574802053692941.07203127640034e-050.000278097055330291
TBP#690883.706770687096392.80450451364125e-050.000592674315864383
THAP1#55145311.76342922606920.001607377924306930.0101231950212079
YY1#752884.911170749853862.95299276601526e-060.000101117249668809



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C986&oldid=2251810"