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Coexpression cluster:C3613: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.99e-14!106;DOID:0050687!1.53e-10!143;DOID:162!1.04e-07!235;DOID:14566!1.24e-07!239;DOID:193!1.66e-07!29
|ontology_enrichment_disease=DOID:305!3.99e-14!106;DOID:0050687!1.53e-10!143;DOID:162!1.04e-07!235;DOID:14566!1.24e-07!239;DOID:193!1.66e-07!29
|ontology_enrichment_uberon=UBERON:0005743!3.62e-19!86;UBERON:0001017!1.12e-18!82;UBERON:0000073!4.92e-17!94;UBERON:0001016!4.92e-17!94;UBERON:0004121!2.56e-15!169;UBERON:0000955!8.85e-15!69;UBERON:0006238!8.85e-15!69;UBERON:0000064!1.08e-14!219;UBERON:0001049!1.75e-14!57;UBERON:0005068!1.75e-14!57;UBERON:0006241!1.75e-14!57;UBERON:0007135!1.75e-14!57;UBERON:0000924!3.77e-14!173;UBERON:0006601!3.77e-14!173;UBERON:0000033!8.98e-13!123;UBERON:0002616!1.95e-12!59;UBERON:0003075!2.42e-12!86;UBERON:0007284!2.42e-12!86;UBERON:0002020!3.25e-11!34;UBERON:0003528!3.25e-11!34;UBERON:0001893!3.92e-11!34;UBERON:0002780!4.74e-11!41;UBERON:0001890!4.74e-11!41;UBERON:0006240!4.74e-11!41;UBERON:0000153!5.27e-11!129;UBERON:0007811!5.27e-11!129;UBERON:0002346!7.40e-11!90;UBERON:0002791!8.61e-11!33;UBERON:0003080!3.92e-10!42;UBERON:0001869!4.99e-10!32;UBERON:0003056!1.27e-09!61;UBERON:0000062!4.22e-08!511;UBERON:0000475!6.61e-08!365;UBERON:0001737!1.32e-07!9;UBERON:0000481!1.36e-07!347;UBERON:0000956!1.43e-07!25;UBERON:0000203!1.43e-07!25;UBERON:0000922!3.30e-07!612;UBERON:0002619!8.03e-07!22
|ontology_enrichment_uberon=UBERON:0005743!3.62e-19!86;UBERON:0001017!1.12e-18!82;UBERON:0000073!4.92e-17!94;UBERON:0001016!4.92e-17!94;UBERON:0004121!2.56e-15!169;UBERON:0000955!8.85e-15!69;UBERON:0006238!8.85e-15!69;UBERON:0000064!1.08e-14!219;UBERON:0001049!1.75e-14!57;UBERON:0005068!1.75e-14!57;UBERON:0006241!1.75e-14!57;UBERON:0007135!1.75e-14!57;UBERON:0000924!3.77e-14!173;UBERON:0006601!3.77e-14!173;UBERON:0000033!8.98e-13!123;UBERON:0002616!1.95e-12!59;UBERON:0003075!2.42e-12!86;UBERON:0007284!2.42e-12!86;UBERON:0002020!3.25e-11!34;UBERON:0003528!3.25e-11!34;UBERON:0001893!3.92e-11!34;UBERON:0002780!4.74e-11!41;UBERON:0001890!4.74e-11!41;UBERON:0006240!4.74e-11!41;UBERON:0000153!5.27e-11!129;UBERON:0007811!5.27e-11!129;UBERON:0002346!7.40e-11!90;UBERON:0002791!8.61e-11!33;UBERON:0003080!3.92e-10!42;UBERON:0001869!4.99e-10!32;UBERON:0003056!1.27e-09!61;UBERON:0000062!4.22e-08!511;UBERON:0000475!6.61e-08!365;UBERON:0001737!1.32e-07!9;UBERON:0000481!1.36e-07!347;UBERON:0000956!1.43e-07!25;UBERON:0000203!1.43e-07!25;UBERON:0000922!3.30e-07!612;UBERON:0002619!8.03e-07!22
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}}
}}

Revision as of 12:38, 5 September 2012


Full id: C3613_optic_Hep2_corpus_lens_Mesenchymal_globus_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr17:20059323..20059342,+p4@SPECC1
Hg19::chr17:20059346..20059355,+p5@SPECC1
Hg19::chr17:20059358..20059401,+p1@SPECC1


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.22e-19254
endo-epithelial cell5.06e-0743
Uber Anatomy
Ontology termp-valuen
central nervous system1.12e-1882
regional part of nervous system4.92e-1794
nervous system4.92e-1794
ectoderm-derived structure2.56e-15169
brain8.85e-1569
future brain8.85e-1569
organ part1.08e-14219
neural tube1.75e-1457
neural rod1.75e-1457
future spinal cord1.75e-1457
neural keel1.75e-1457
ectoderm3.77e-14173
presumptive ectoderm3.77e-14173
head8.98e-13123
regional part of brain1.95e-1259
neural plate2.42e-1286
presumptive neural plate2.42e-1286
gray matter3.25e-1134
brain grey matter3.25e-1134
telencephalon3.92e-1134
regional part of forebrain4.74e-1141
forebrain4.74e-1141
future forebrain4.74e-1141
anterior region of body5.27e-11129
craniocervical region5.27e-11129
neurectoderm7.40e-1190
regional part of telencephalon8.61e-1133
anterior neural tube3.92e-1042
cerebral hemisphere4.99e-1032
pre-chordal neural plate1.27e-0961
organ4.22e-08511
organism subdivision6.61e-08365
larynx1.32e-079
multi-tissue structure1.36e-07347
cerebral cortex1.43e-0725
pallium1.43e-0725
embryo3.30e-07612
regional part of cerebral cortex8.03e-0722
Disease
Ontology termp-valuen
carcinoma3.99e-14106
cell type cancer1.53e-10143
cancer1.04e-07235
disease of cellular proliferation1.24e-07239
reproductive organ cancer1.66e-0729


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#90536.336201576962630.003930750035764890.0189811172084913
E2F1#186934.907389214879320.008460985347239390.0324838013704494
E2F6#187635.017155731697390.00791769806886330.0321644742546973
EGR1#195834.988179094810140.008056488137383440.0320184011788953
ELF1#199734.258097958807540.01295179875054610.0461631598426143
IRF1#365937.63716375356390.002244692747297240.012791698905166
JUND#372736.994663941871030.002921845042734990.01565457212426
MEF2A#4205318.74323090964410.0001518243905622470.00195011530266025
MYC#460935.22228187160940.007020843755740150.0294147104061997
NFKB1#479035.488063424193840.006049381815655430.0269317271599488
PAX5#507936.669565531177830.003370290999677260.0172755740719163
POU2F2#545239.106124057742520.001324165192682130.00881418027779025
SMARCB1#6598318.25271578115740.000164397760679890.0020290165123667
SP1#666735.69838137814090.005403962701712170.0246165857113498
TAF7#6879311.43306940492390.0006690181981945830.00542144565496928
TCF12#6938310.63446490218640.0008313523990202070.00628806584597852
ZEB1#6935316.88843201754390.0002075486917327580.00242571372156194
ZNF143#7702313.50087655222790.0004062804962997170.00388709497554471



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.

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