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Coexpression cluster:C2238: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle
|full_id=C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle
|gostat_on_coexpression_clusters=GO:0003677!DNA binding!0.0403705274123335!7697;340252;83591$GO:0008270!zinc ion binding!0.0403705274123335!7697;340252;83591$GO:0046914!transition metal ion binding!0.0440143862349641!7697;340252;83591$GO:0005634!nucleus!0.0472393264798422!7697;340252;83591$GO:0003676!nucleic acid binding!0.0472393264798422!7697;340252;83591$GO:0043169!cation binding!0.0472393264798422!7697;340252;83591$GO:0046872!metal ion binding!0.0472393264798422!7697;340252;83591$GO:0043167!ion binding!0.0472393264798422!7697;340252;83591
|gostat_on_coexpression_clusters=GO:0003677!DNA binding!0.0403705274123335!7697;340252;83591$GO:0008270!zinc ion binding!0.0403705274123335!7697;340252;83591$GO:0046914!transition metal ion binding!0.0440143862349641!7697;340252;83591$GO:0005634!nucleus!0.0472393264798422!7697;340252;83591$GO:0003676!nucleic acid binding!0.0472393264798422!7697;340252;83591$GO:0043169!cation binding!0.0472393264798422!7697;340252;83591$GO:0046872!metal ion binding!0.0472393264798422!7697;340252;83591$GO:0043167!ion binding!0.0472393264798422!7697;340252;83591

Revision as of 14:56, 12 September 2012


Full id: C2238_cerebellum_spinal_occipital_parietal_putamen_medial_middle



Phase1 CAGE Peaks

Hg19::chr12:72058060..72058101,+p5@THAP2
Hg19::chr7:64023410..64023428,-p2@ZNF680
Hg19::chr7:64023441..64023462,-p1@ZNF680
Hg19::chr7:64254793..64254813,+p1@ZNF138


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:0003677DNA binding0.0403705274123335
GO:0008270zinc ion binding0.0403705274123335
GO:0046914transition metal ion binding0.0440143862349641
GO:0005634nucleus0.0472393264798422
GO:0003676nucleic acid binding0.0472393264798422
GO:0043169cation binding0.0472393264798422
GO:0046872metal ion binding0.0472393264798422
GO:0043167ion binding0.0472393264798422



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
lymphocyte3.50e-1053
common lymphoid progenitor3.50e-1053
lymphoid lineage restricted progenitor cell9.23e-1052
Uber Anatomy
Ontology termp-valuen
adult organism4.01e-33115
central nervous system7.40e-3182
regional part of nervous system1.91e-2994
nervous system1.91e-2994
neural tube1.63e-2857
neural rod1.63e-2857
future spinal cord1.63e-2857
neural keel1.63e-2857
brain6.25e-2669
future brain6.25e-2669
regional part of forebrain2.91e-2441
forebrain2.91e-2441
future forebrain2.91e-2441
anterior neural tube2.95e-2442
regional part of brain1.43e-2359
neurectoderm5.53e-2290
neural plate2.93e-2186
presumptive neural plate2.93e-2186
gray matter2.51e-2034
brain grey matter2.51e-2034
telencephalon4.18e-2034
regional part of telencephalon1.46e-1933
cerebral hemisphere5.90e-1932
pre-chordal neural plate8.12e-1661
cerebral cortex1.15e-1425
pallium1.15e-1425
regional part of cerebral cortex4.59e-1422
anterior region of body1.41e-13129
craniocervical region1.41e-13129
ectoderm3.04e-13173
presumptive ectoderm3.04e-13173
neocortex8.82e-1320
ectoderm-derived structure1.42e-12169
head2.54e-12123
basal ganglion3.29e-079
nuclear complex of neuraxis3.29e-079
aggregate regional part of brain3.29e-079
collection of basal ganglia3.29e-079
cerebral subcortex3.29e-079
nucleus of brain3.64e-079
neural nucleus3.64e-079
Disease
Ontology termp-valuen
cancer3.06e-10235
disease of cellular proliferation1.58e-09239
organ system cancer4.13e-08137
hematologic cancer7.98e-0751
immune system cancer7.98e-0751


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
BCLAF1#9774210.82632380506090.01202203816432580.0436476967198784
CHD2#1106410.34402283411698.73193255208051e-050.0012893458275226
E2F4#187439.501045236463330.001850751034728270.0109246926646688
ELF1#199744.258097958807540.003041525565781240.0160658450619374
FOS#235336.74846648167080.005032452776317940.0234583501676353
GABPB1#255347.067683836182170.0004006876864423170.00389894915534791
HEY1#2346244.040111043105710.00375304636917980.0185668329188939
IRF1#365947.63716375356390.0002938853996185490.00306992370981813
IRF3#3661335.23646415861723.79279212646878e-050.000719555707350178
NFYA#4800313.81918552487290.0006132411806734510.00508505721860695
NFYB#4801312.56984494015230.000811456397697350.00618506018968863
PBX3#5090316.43588451505810.0003669431395554610.00365679146488863
RFX5#5993412.04791082719514.74457429336527e-050.000825726703257416
SIN3A#2594245.408884726815140.001168172384885160.00794909797400448
SP1#666745.69838137814090.0009482606065333980.00683332570797913
SP2#6668319.61514787038350.0002171004269245340.00248506701968121
SPI1#668836.153242631392040.006580387113059030.0280945568514746
TAF1#687243.343046285745290.008005664898701650.0321491766199678
TBP#690843.706770687096390.005296377814784350.0243688445569524
TCF7L2#6934410.77017656313737.42969445082454e-050.00115194456465211
ZNF263#1012736.166381227758010.006539814347975980.0279636303250057



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.