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Coexpression cluster:C2739: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513104405376378!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818763755022838!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106667755320206!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998285982441874!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101584067728525!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234852528690081!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000311665097490246!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129725891806444
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513104405376378!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818763755022838!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106667755320206!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00998285982441874!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101584067728525!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234852528690081!NFYB#4801;4:16.7597932535365:1.26678572070404e-05:0.000311665097490246!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129725891806444
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}}
}}

Revision as of 15:41, 26 November 2012


Full id: C2739_retina_cerebellum_Hepatocyte_salivary_submaxillary_parotid_small



Phase1 CAGE Peaks

Hg19::chr3:39851061..39851085,+p4@MYRIP
Hg19::chr3:39851094..39851151,+p1@MYRIP
Hg19::chr3:39851154..39851165,+p6@MYRIP
Hg19::chr3:39851170..39851195,+p3@MYRIP


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 organism3.56e-59114
neural tube3.32e-3756
neural rod3.32e-3756
future spinal cord3.32e-3756
neural keel3.32e-3756
regional part of nervous system1.32e-3453
regional part of brain1.32e-3453
central nervous system7.73e-3381
nervous system1.23e-3289
regional part of forebrain9.19e-2941
forebrain9.19e-2941
anterior neural tube9.19e-2941
future forebrain9.19e-2941
brain1.54e-2668
future brain1.54e-2668
brain grey matter2.10e-2534
gray matter2.10e-2534
neural plate2.16e-2582
presumptive neural plate2.16e-2582
telencephalon2.74e-2534
anatomical cluster1.89e-24373
cerebral hemisphere1.02e-2332
regional part of telencephalon1.65e-2332
neurectoderm3.19e-2386
tube1.17e-22192
anatomical conduit1.59e-22240
regional part of cerebral cortex4.74e-2222
organ system subdivision5.86e-22223
neocortex2.53e-2020
pre-chordal neural plate9.76e-1961
cerebral cortex2.25e-1825
pallium2.25e-1825
ecto-epithelium6.41e-18104
structure with developmental contribution from neural crest3.05e-16132
ectoderm-derived structure1.33e-13171
ectoderm1.33e-13171
presumptive ectoderm1.33e-13171
epithelium6.74e-12306
cell layer1.80e-11309
blood vessel endothelium3.74e-1018
endothelium3.74e-1018
cardiovascular system endothelium3.74e-1018
posterior neural tube1.73e-0915
chordal neural plate1.73e-0915
multi-cellular organism6.66e-09656
anatomical system1.13e-08624
anatomical group1.41e-08625
embryo1.66e-08592
neural nucleus1.70e-089
nucleus of brain1.70e-089
germ layer2.79e-08560
germ layer / neural crest2.79e-08560
embryonic tissue2.79e-08560
presumptive structure2.79e-08560
germ layer / neural crest derived structure2.79e-08560
epiblast (generic)2.79e-08560
embryonic structure2.88e-08564
basal ganglion3.14e-089
nuclear complex of neuraxis3.14e-089
aggregate regional part of brain3.14e-089
collection of basal ganglia3.14e-089
cerebral subcortex3.14e-089
segmental subdivision of nervous system6.14e-0813
developing anatomical structure1.19e-07581
multi-tissue structure1.39e-07342
temporal lobe1.94e-076
simple squamous epithelium2.14e-0722
brainstem2.19e-076
gyrus2.39e-076
segmental subdivision of hindbrain4.01e-0712
hindbrain4.01e-0712
presumptive hindbrain4.01e-0712


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#90546.336201576962630.0006203100587215640.00513104405376378
CTCF#1066445.360256373075030.001211145381643620.00818763755022838
E2F1#186944.907389214879320.001724022357361790.0106667755320206
E2F6#187645.017155731697390.00157802193473060.00998285982441874
EGR1#195844.988179094810140.001615011500076050.0101584067728525
NFYA#4800418.42558069983058.67100748407158e-060.000234852528690081
NFYB#4801416.75979325353651.26678572070404e-050.000311665097490246
RAD21#5885410.35503389545638.6948481184721e-050.00129725891806444



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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