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Coexpression cluster:C1815: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!2.68e-31!115;UBERON:0000073!1.07e-22!94;UBERON:0001016!1.07e-22!94;UBERON:0005743!1.01e-21!86;UBERON:0001017!1.06e-21!82;UBERON:0001049!8.77e-21!57;UBERON:0005068!8.77e-21!57;UBERON:0006241!8.77e-21!57;UBERON:0007135!8.77e-21!57;UBERON:0002616!2.30e-18!59;UBERON:0002346!3.59e-18!90;UBERON:0003080!1.50e-17!42;UBERON:0002780!1.89e-17!41;UBERON:0001890!1.89e-17!41;UBERON:0006240!1.89e-17!41;UBERON:0003075!3.98e-17!86;UBERON:0007284!3.98e-17!86;UBERON:0000955!5.37e-17!69;UBERON:0006238!5.37e-17!69;UBERON:0002020!3.63e-14!34;UBERON:0003528!3.63e-14!34;UBERON:0001893!8.31e-14!34;UBERON:0002791!1.18e-13!33;UBERON:0003056!1.21e-13!61;UBERON:0001869!4.89e-13!32;UBERON:0000924!5.17e-13!173;UBERON:0006601!5.17e-13!173;UBERON:0004121!3.78e-12!169;UBERON:0000153!8.64e-12!129;UBERON:0007811!8.64e-12!129;UBERON:0000033!2.58e-10!123;UBERON:0000956!6.06e-10!25;UBERON:0000203!6.06e-10!25;UBERON:0002619!9.52e-10!22;UBERON:0001950!6.97e-09!20
|ontology_enrichment_uberon=UBERON:0007023!2.68e-31!115;UBERON:0000073!1.07e-22!94;UBERON:0001016!1.07e-22!94;UBERON:0005743!1.01e-21!86;UBERON:0001017!1.06e-21!82;UBERON:0001049!8.77e-21!57;UBERON:0005068!8.77e-21!57;UBERON:0006241!8.77e-21!57;UBERON:0007135!8.77e-21!57;UBERON:0002616!2.30e-18!59;UBERON:0002346!3.59e-18!90;UBERON:0003080!1.50e-17!42;UBERON:0002780!1.89e-17!41;UBERON:0001890!1.89e-17!41;UBERON:0006240!1.89e-17!41;UBERON:0003075!3.98e-17!86;UBERON:0007284!3.98e-17!86;UBERON:0000955!5.37e-17!69;UBERON:0006238!5.37e-17!69;UBERON:0002020!3.63e-14!34;UBERON:0003528!3.63e-14!34;UBERON:0001893!8.31e-14!34;UBERON:0002791!1.18e-13!33;UBERON:0003056!1.21e-13!61;UBERON:0001869!4.89e-13!32;UBERON:0000924!5.17e-13!173;UBERON:0006601!5.17e-13!173;UBERON:0004121!3.78e-12!169;UBERON:0000153!8.64e-12!129;UBERON:0007811!8.64e-12!129;UBERON:0000033!2.58e-10!123;UBERON:0000956!6.06e-10!25;UBERON:0000203!6.06e-10!25;UBERON:0002619!9.52e-10!22;UBERON:0001950!6.97e-09!20
|pathway_enrichment=4.64055626633526e-10;2.93747211659022e-07;5;390;{ASH2L,391} (Static Module):NA
|pathway_enrichment=4.64055626633526e-10;2.93747211659022e-07;5;390;{ASH2L,391} (Static Module):NA
|tf_chipseq_enrich=CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319558518886259!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00573232062378663!FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389166227027733!GATA2#2624;4:10.1959453868432:0.000177544777760982:0.00215711947936007!GATA3#2625;3:16.3419098143236:0.000467886519508923:0.00430192800519345!IRF3#3661;3:28.1891713268937:9.33088977565955e-05:0.00135631008668073!NFYA#4800;4:14.7404645598644:4.14733626928016e-05:0.000752246704806096!NFYB#4801;4:13.4078346028292:6.03169250119439e-05:0.00099141317773409!PBX3#5090;3:13.1487076120465:0.000886046932280843:0.00660371480485827!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542587221132184!SP1#6667;5:5.6983813781409:0.00016639184371255:0.00204324488718342!SP2#6668;2:10.4614121975379:0.0135319118334714:0.0477823761698589!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135395830702401!TAF7#6879;4:9.14645552393913:0.000272066287241299:0.00290297619260258!TBP#6908;5:3.70677068709639:0.00142875510672112:0.009189417082821
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}}
}}

Revision as of 11:33, 5 September 2012


Full id: C1815_CD4_cerebellum_cord_CD19_pineal_parietal_pituitary



Phase1 CAGE Peaks

Hg19::chr19:19932513..19932569,-p1@ZNF506
Hg19::chr19:19976634..19976677,+p2@ZNF253
Hg19::chr19:20748574..20748599,-p1@ZNF737
Hg19::chr19:22018966..22019001,-p1@ZNF43
Hg19::chr4:331578..331615,+p1@ZNF141


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


p.valueFDRnGenesnPathwayName
4.64055626633526e-102.93747211659022e-075390{ASH2L,391} (Static Module):NA



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:0006355regulation of transcription, DNA-dependent0.000846431334884364
GO:0006351transcription, DNA-dependent0.000846431334884364
GO:0032774RNA biosynthetic process0.000846431334884364
GO:0003677DNA binding0.000846431334884364
GO:0045449regulation of transcription0.000846431334884364
GO:0005730nucleolus0.000846431334884364
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.000846431334884364
GO:0006350transcription0.000846431334884364
GO:0010468regulation of gene expression0.000846431334884364
GO:0031323regulation of cellular metabolic process0.000846431334884364
GO:0019222regulation of metabolic process0.000846431334884364
GO:0016070RNA metabolic process0.000846431334884364
GO:0008270zinc ion binding0.000846431334884364
GO:0046914transition metal ion binding0.00151449307368346
GO:0010467gene expression0.00216810207862511
GO:0050794regulation of cellular process0.00243180912712297
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00252885068474743
GO:0005634nucleus0.00274969000691553
GO:0050789regulation of biological process0.00274969000691553
GO:0003676nucleic acid binding0.00303959206670695
GO:0043169cation binding0.00311902856622841
GO:0065007biological regulation0.00343002124051222
GO:0046872metal ion binding0.00350277187617976
GO:0043167ion binding0.00359037836362785
GO:0031981nuclear lumen0.0047146401294312
GO:0043283biopolymer metabolic process0.00562041980758463
GO:0043231intracellular membrane-bound organelle0.00744887228320251
GO:0043227membrane-bound organelle0.00744887228320251
GO:0003704specific RNA polymerase II transcription factor activity0.00744887228320251
GO:0031974membrane-enclosed lumen0.00744887228320251
GO:0043233organelle lumen0.00744887228320251
GO:0044428nuclear part0.0093458991010516
GO:0043229intracellular organelle0.0145414453986348
GO:0043226organelle0.0145414453986348
GO:0043170macromolecule metabolic process0.016205067423626
GO:0044237cellular metabolic process0.026309483769755
GO:0044238primary metabolic process0.026383330268527
GO:0044424intracellular part0.0272869829045711
GO:0016564transcription repressor activity0.0313615375688903
GO:0003702RNA polymerase II transcription factor activity0.0397506666735284
GO:0005622intracellular0.0442867803553934
GO:0043232intracellular non-membrane-bound organelle0.0448997808200877
GO:0043228non-membrane-bound organelle0.0448997808200877



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 organism2.68e-31115
regional part of nervous system1.07e-2294
nervous system1.07e-2294
central nervous system1.06e-2182
neural tube8.77e-2157
neural rod8.77e-2157
future spinal cord8.77e-2157
neural keel8.77e-2157
regional part of brain2.30e-1859
neurectoderm3.59e-1890
anterior neural tube1.50e-1742
regional part of forebrain1.89e-1741
forebrain1.89e-1741
future forebrain1.89e-1741
neural plate3.98e-1786
presumptive neural plate3.98e-1786
brain5.37e-1769
future brain5.37e-1769
gray matter3.63e-1434
brain grey matter3.63e-1434
telencephalon8.31e-1434
regional part of telencephalon1.18e-1333
pre-chordal neural plate1.21e-1361
cerebral hemisphere4.89e-1332
ectoderm5.17e-13173
presumptive ectoderm5.17e-13173
ectoderm-derived structure3.78e-12169
anterior region of body8.64e-12129
craniocervical region8.64e-12129
head2.58e-10123
cerebral cortex6.06e-1025
pallium6.06e-1025
regional part of cerebral cortex9.52e-1022
neocortex6.97e-0920


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
CHD2#110636.206413700470110.007774550126275590.0319558518886259
ELF1#199754.258097958807540.0007142416939776840.00573232062378663
FOS#235358.99795530889441.69470025615156e-050.000389166227027733
GATA2#2624410.19594538684320.0001775447777609820.00215711947936007
GATA3#2625316.34190981432360.0004678865195089230.00430192800519345
IRF3#3661328.18917132689379.33088977565955e-050.00135631008668073
NFYA#4800414.74046455986444.14733626928016e-050.000752246704806096
NFYB#4801413.40783460282926.03169250119439e-050.00099141317773409
PBX3#5090313.14870761204650.0008860469322808430.00660371480485827
POU2F2#545247.284899246194020.0006631223288743860.00542587221132184
SP1#666755.69838137814090.000166391843712550.00204324488718342
SP2#6668210.46141219753790.01353191183347140.0477823761698589
TAF1#687253.343046285745290.002394600090870310.0135395830702401
TAF7#687949.146455523939130.0002720662872412990.00290297619260258
TBP#690853.706770687096390.001428755106721120.009189417082821



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.