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Coexpression cluster:C4702: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.60e-31!115;UBERON:0001049!2.36e-27!57;UBERON:0005068!2.36e-27!57;UBERON:0006241!2.36e-27!57;UBERON:0007135!2.36e-27!57;UBERON:0001017!7.50e-23!82;UBERON:0002616!7.78e-22!59;UBERON:0005743!1.72e-21!86;UBERON:0003080!3.92e-21!42;UBERON:0000073!6.97e-21!94;UBERON:0001016!6.97e-21!94;UBERON:0002780!8.73e-21!41;UBERON:0001890!8.73e-21!41;UBERON:0006240!8.73e-21!41;UBERON:0000955!1.37e-20!69;UBERON:0006238!1.37e-20!69;UBERON:0003075!1.54e-19!86;UBERON:0007284!1.54e-19!86;UBERON:0002346!8.22e-19!90;UBERON:0001893!1.18e-17!34;UBERON:0002020!1.63e-17!34;UBERON:0003528!1.63e-17!34;UBERON:0002791!4.76e-17!33;UBERON:0001869!2.47e-16!32;UBERON:0003056!4.83e-13!61;UBERON:0002619!5.31e-13!22;UBERON:0000956!2.37e-12!25;UBERON:0000203!2.37e-12!25;UBERON:0001950!4.25e-12!20;UBERON:0000025!3.59e-10!194;UBERON:0004111!9.89e-10!241;UBERON:0000153!1.12e-09!129;UBERON:0007811!1.12e-09!129;UBERON:0000033!8.92e-09!123;UBERON:0000477!1.29e-07!286;UBERON:0004121!1.42e-07!169;UBERON:0001986!1.62e-07!18;UBERON:0004638!1.62e-07!18;UBERON:0004852!1.62e-07!18;UBERON:0000924!1.86e-07!173;UBERON:0006601!1.86e-07!173;UBERON:0003076!2.13e-07!15;UBERON:0003057!2.13e-07!15;UBERON:0000487!6.28e-07!22;UBERON:0002308!9.99e-07!9;UBERON:0000125!9.99e-07!9
|ontology_enrichment_uberon=UBERON:0007023!3.60e-31!115;UBERON:0001049!2.36e-27!57;UBERON:0005068!2.36e-27!57;UBERON:0006241!2.36e-27!57;UBERON:0007135!2.36e-27!57;UBERON:0001017!7.50e-23!82;UBERON:0002616!7.78e-22!59;UBERON:0005743!1.72e-21!86;UBERON:0003080!3.92e-21!42;UBERON:0000073!6.97e-21!94;UBERON:0001016!6.97e-21!94;UBERON:0002780!8.73e-21!41;UBERON:0001890!8.73e-21!41;UBERON:0006240!8.73e-21!41;UBERON:0000955!1.37e-20!69;UBERON:0006238!1.37e-20!69;UBERON:0003075!1.54e-19!86;UBERON:0007284!1.54e-19!86;UBERON:0002346!8.22e-19!90;UBERON:0001893!1.18e-17!34;UBERON:0002020!1.63e-17!34;UBERON:0003528!1.63e-17!34;UBERON:0002791!4.76e-17!33;UBERON:0001869!2.47e-16!32;UBERON:0003056!4.83e-13!61;UBERON:0002619!5.31e-13!22;UBERON:0000956!2.37e-12!25;UBERON:0000203!2.37e-12!25;UBERON:0001950!4.25e-12!20;UBERON:0000025!3.59e-10!194;UBERON:0004111!9.89e-10!241;UBERON:0000153!1.12e-09!129;UBERON:0007811!1.12e-09!129;UBERON:0000033!8.92e-09!123;UBERON:0000477!1.29e-07!286;UBERON:0004121!1.42e-07!169;UBERON:0001986!1.62e-07!18;UBERON:0004638!1.62e-07!18;UBERON:0004852!1.62e-07!18;UBERON:0000924!1.86e-07!173;UBERON:0006601!1.86e-07!173;UBERON:0003076!2.13e-07!15;UBERON:0003057!2.13e-07!15;UBERON:0000487!6.28e-07!22;UBERON:0002308!9.99e-07!9;UBERON:0000125!9.99e-07!9
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}}
}}

Revision as of 13:58, 5 September 2012


Full id: C4702_bone_corpus_Endothelial_optic_diencephalon_thalamus_Wilms



Phase1 CAGE Peaks

Hg19::chr7:86688940..86688951,-p4@KIAA1324L
Hg19::chr7:86688955..86688988,-p1@KIAA1324L
Hg19::chr7:86688990..86689026,-p2@KIAA1324L


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 organism3.60e-31115
neural tube2.36e-2757
neural rod2.36e-2757
future spinal cord2.36e-2757
neural keel2.36e-2757
central nervous system7.50e-2382
regional part of brain7.78e-2259
anterior neural tube3.92e-2142
regional part of nervous system6.97e-2194
nervous system6.97e-2194
regional part of forebrain8.73e-2141
forebrain8.73e-2141
future forebrain8.73e-2141
brain1.37e-2069
future brain1.37e-2069
neural plate1.54e-1986
presumptive neural plate1.54e-1986
neurectoderm8.22e-1990
telencephalon1.18e-1734
gray matter1.63e-1734
brain grey matter1.63e-1734
regional part of telencephalon4.76e-1733
cerebral hemisphere2.47e-1632
pre-chordal neural plate4.83e-1361
regional part of cerebral cortex5.31e-1322
cerebral cortex2.37e-1225
pallium2.37e-1225
neocortex4.25e-1220
tube3.59e-10194
anatomical conduit9.89e-10241
anterior region of body1.12e-09129
craniocervical region1.12e-09129
head8.92e-09123
anatomical cluster1.29e-07286
ectoderm-derived structure1.42e-07169
endothelium1.62e-0718
blood vessel endothelium1.62e-0718
cardiovascular system endothelium1.62e-0718
ectoderm1.86e-07173
presumptive ectoderm1.86e-07173
posterior neural tube2.13e-0715
chordal neural plate2.13e-0715
simple squamous epithelium6.28e-0722
nucleus of brain9.99e-079
neural nucleus9.99e-079


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#90536.336201576962630.003930750035764890.0191145692128905
CTCF#1066435.360256373075030.0064925092527670.0281333986328825
CTCFL#140690319.74647435897440.0001298372005551160.00172344527056124
E2F1#186934.907389214879320.008460985347239390.0327753736389724
E2F6#187635.017155731697390.00791769806886330.032430640388031
EBF1#187938.9064668465690.00141523283560980.00919302787151713
EGR1#195834.988179094810140.008056488137383440.0322478753863326
FOXA1#3169311.08141974938550.000734755275698670.00584263029074869
HMGN3#932438.178547723350590.001827766942164210.0109211140038153
IRF1#365937.63716375356390.002244692747297240.0128738860974726
RAD21#5885310.35503389545630.0009004912073565420.00668655536474297
SIN3A#2594235.408884726815140.006318961977991520.0278282129462136
SMC3#9126315.04493284493280.0002935825420371870.00310810614372243
TAF7#6879311.43306940492390.0006690181981945830.00545743900658002
TCF12#6938310.63446490218640.0008313523990202070.006320105779682
ZBTB7A#5134137.35190930787590.002516255860282270.0140916534823325



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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