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Coexpression cluster:C3044: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0006110!regulation of glycolysis!0.0153060473107074!11319$GO:0009894!regulation of catabolic process!0.0407993044316206!11319$GO:0005086!ARF guanyl-nucleotide exchange factor activity!0.0407993044316206!8925
|gostat_on_coexpression_clusters=GO:0006110!regulation of glycolysis!0.0153060473107074!11319$GO:0009894!regulation of catabolic process!0.0407993044316206!11319$GO:0005086!ARF guanyl-nucleotide exchange factor activity!0.0407993044316206!8925
|id=C3044
|id=C3044
|ontology_enrichment_celltype=CL:0000037!1.84e-30!172;CL:0000566!1.84e-30!172;CL:0002032!3.39e-27!165;CL:0000837!3.39e-27!165;CL:0000738!1.25e-26!140;CL:0000988!1.07e-25!182;CL:0002031!5.10e-20!124;CL:0002087!4.48e-18!119;CL:0000838!2.10e-14!52;CL:0000542!3.32e-14!53;CL:0000051!3.32e-14!53;CL:0000763!2.34e-13!112;CL:0000049!2.34e-13!112;CL:0000791!4.08e-11!18;CL:0000789!4.08e-11!18;CL:0002420!4.08e-11!18;CL:0002419!4.08e-11!18;CL:0000790!4.08e-11!18;CL:0000766!2.46e-09!76;CL:0000084!4.66e-09!25;CL:0000827!4.66e-09!25;CL:0000625!1.49e-07!11;CL:0000557!5.21e-07!71;CL:0000839!6.35e-07!70
|ontology_enrichment_celltype=CL:0000037!1.26e-29!168;CL:0000566!1.26e-29!168;CL:0002032!2.73e-26!161;CL:0000837!2.73e-26!161;CL:0000988!3.41e-26!177;CL:0000738!7.08e-25!136;CL:0002031!1.39e-18!120;CL:0002087!4.89e-17!115;CL:0002242!4.98e-14!55;CL:0000763!1.77e-13!108;CL:0000049!1.77e-13!108;CL:0000838!3.48e-13!52;CL:0000542!5.56e-13!53;CL:0000051!5.56e-13!53;CL:0000791!4.59e-11!18;CL:0000789!4.59e-11!18;CL:0002420!4.59e-11!18;CL:0002419!4.59e-11!18;CL:0000790!4.59e-11!18;CL:0000766!5.51e-09!72;CL:0000084!1.52e-08!25;CL:0000827!1.52e-08!25;CL:0000625!1.77e-07!11
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.13e-37!115;UBERON:0001049!3.30e-17!57;UBERON:0005068!3.30e-17!57;UBERON:0006241!3.30e-17!57;UBERON:0007135!3.30e-17!57;UBERON:0002780!2.83e-16!41;UBERON:0001890!2.83e-16!41;UBERON:0006240!2.83e-16!41;UBERON:0003080!5.36e-16!42;UBERON:0002616!6.00e-14!59;UBERON:0001893!1.59e-13!34;UBERON:0000955!1.76e-13!69;UBERON:0006238!1.76e-13!69;UBERON:0002020!2.76e-13!34;UBERON:0003528!2.76e-13!34;UBERON:0001017!3.73e-13!82;UBERON:0002791!4.87e-13!33;UBERON:0001869!1.19e-12!32;UBERON:0000073!6.68e-12!94;UBERON:0001016!6.68e-12!94;UBERON:0005743!7.46e-12!86;UBERON:0002619!3.17e-11!22;UBERON:0001950!2.51e-10!20;UBERON:0000956!1.44e-09!25;UBERON:0000203!1.44e-09!25;UBERON:0002390!1.61e-09!102;UBERON:0003061!1.61e-09!102;UBERON:0002346!3.40e-08!90;UBERON:0002193!4.51e-08!112;UBERON:0003075!9.47e-08!86;UBERON:0007284!9.47e-08!86
|ontology_enrichment_uberon=UBERON:0007023!5.83e-35!114;UBERON:0001049!1.39e-15!56;UBERON:0005068!1.39e-15!56;UBERON:0006241!1.39e-15!56;UBERON:0007135!1.39e-15!56;UBERON:0000073!6.73e-15!53;UBERON:0002616!6.73e-15!53;UBERON:0002780!2.92e-14!41;UBERON:0001890!2.92e-14!41;UBERON:0003080!2.92e-14!41;UBERON:0006240!2.92e-14!41;UBERON:0000955!2.30e-12!68;UBERON:0006238!2.30e-12!68;UBERON:0001017!3.60e-12!81;UBERON:0001016!8.97e-12!89;UBERON:0001893!2.57e-11!34;UBERON:0003528!3.41e-11!34;UBERON:0002020!3.41e-11!34;UBERON:0002791!1.70e-10!32;UBERON:0001869!2.35e-10!32;UBERON:0002390!2.99e-09!98;UBERON:0003061!2.99e-09!98;UBERON:0002619!3.66e-09!22;UBERON:0001950!2.14e-08!20;UBERON:0002193!7.82e-08!108;UBERON:0000956!1.23e-07!25;UBERON:0000203!1.23e-07!25;UBERON:0002346!1.28e-07!86;UBERON:0003075!3.54e-07!82;UBERON:0007284!3.54e-07!82
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.02594242156343!BRCA1#672;3:20.1842306432238:0.000121570486027164:0.00163891828968516!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658204764524753!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0318982320335199!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459920747240245!ELK4#2005;2:10.823787772312:0.0109128471951648:0.0401708320955807!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00386809792759555!MEF2A#4205;2:12.495487273096:0.00823502947802974:0.0324697313370563!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0268516038694903!NR3C1#2908;2:9.98201555411536:0.0127847436554717:0.0460089536071745!SIX5#147912;2:11.391143570306:0.00987382008142903:0.037055298267432!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245373879659196!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189465349553334!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327836216883502!ZBTB33#10009;2:21.1098166866541:0.00292859706060324:0.0156274140819713
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}}
}}

Revision as of 14:45, 19 October 2012


Full id: C3044_Eosinophils_CD4_Neutrophils_CD34_CD8_CD19_Natural



Phase1 CAGE Peaks

Hg19::chr10:74927810..74927834,-p2@ECD
Hg19::chr15:64126110..64126154,-p1@HERC1
Hg19::chr17:47866034..47866060,+p1@KAT7


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:0006110regulation of glycolysis0.0153060473107074
GO:0009894regulation of catabolic process0.0407993044316206
GO:0005086ARF guanyl-nucleotide exchange factor activity0.0407993044316206



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 organism5.83e-35114
neural tube1.39e-1556
neural rod1.39e-1556
future spinal cord1.39e-1556
neural keel1.39e-1556
regional part of nervous system6.73e-1553
regional part of brain6.73e-1553
regional part of forebrain2.92e-1441
forebrain2.92e-1441
anterior neural tube2.92e-1441
future forebrain2.92e-1441
brain2.30e-1268
future brain2.30e-1268
central nervous system3.60e-1281
nervous system8.97e-1289
telencephalon2.57e-1134
brain grey matter3.41e-1134
gray matter3.41e-1134
regional part of telencephalon1.70e-1032
cerebral hemisphere2.35e-1032
hematopoietic system2.99e-0998
blood island2.99e-0998
regional part of cerebral cortex3.66e-0922
neocortex2.14e-0820
hemolymphoid system7.82e-08108
cerebral cortex1.23e-0725
pallium1.23e-0725
neurectoderm1.28e-0786
neural plate3.54e-0782
presumptive neural plate3.54e-0782


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#467214.97544968400580.005768294540793880.02594242156343
BRCA1#672320.18423064322380.0001215704860271640.00163891828968516
CHD2#1106310.34402283411690.0009033701102746880.00658204764524753
EGR1#195834.988179094810140.008056488137383440.0318982320335199
ELF1#199734.258097958807540.01295179875054610.0459920747240245
ELK4#2005210.8237877723120.01091284719516480.0401708320955807
GATA1#2623313.56030814380040.0004009615963782630.00386809792759555
MEF2A#4205212.4954872730960.008235029478029740.0324697313370563
NFKB1#479035.488063424193840.006049381815655430.0268516038694903
NR3C1#290829.982015554115360.01278474365547170.0460089536071745
SIX5#147912211.3911435703060.009873820081429030.037055298267432
SP1#666735.69838137814090.005403962701712170.0245373879659196
USF1#739136.361499277207960.00388404057290560.0189465349553334
YY1#752834.911170749853860.008441455341808260.0327836216883502
ZBTB33#10009221.10981668665410.002928597060603240.0156274140819713



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.