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Coexpression cluster:C4657: Difference between revisions

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|full_id=C4657_corpus_globus_optic_thalamus_medulla_locus_substantia
|full_id=C4657_corpus_globus_optic_thalamus_medulla_locus_substantia
|id=C4657
|id=C4657
|ontology_enrichment_celltype=CL:0002057!1.96e-11!42;CL:0000860!2.21e-09!45;CL:0000766!1.34e-07!76
|ontology_enrichment_celltype=CL:0000860!8.17e-10!42;CL:0002057!8.17e-10!42;CL:0000473!1.20e-07!48;CL:0000234!1.20e-07!48;CL:0000766!2.60e-07!72
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.48e-36!115;UBERON:0001049!1.52e-27!57;UBERON:0005068!1.52e-27!57;UBERON:0006241!1.52e-27!57;UBERON:0007135!1.52e-27!57;UBERON:0002616!3.98e-25!59;UBERON:0000955!1.00e-22!69;UBERON:0006238!1.00e-22!69;UBERON:0003080!6.49e-22!42;UBERON:0003075!7.56e-22!86;UBERON:0007284!7.56e-22!86;UBERON:0002780!2.51e-21!41;UBERON:0001890!2.51e-21!41;UBERON:0006240!2.51e-21!41;UBERON:0001017!4.48e-21!82;UBERON:0005743!8.83e-20!86;UBERON:0002346!8.68e-19!90;UBERON:0000073!4.57e-18!94;UBERON:0001016!4.57e-18!94;UBERON:0003056!9.24e-18!61;UBERON:0000153!9.74e-18!129;UBERON:0007811!9.74e-18!129;UBERON:0000033!1.29e-17!123;UBERON:0002020!2.21e-17!34;UBERON:0003528!2.21e-17!34;UBERON:0001893!2.45e-17!34;UBERON:0002791!9.41e-17!33;UBERON:0000062!3.80e-16!511;UBERON:0001869!5.31e-16!32;UBERON:0000923!6.84e-15!604;UBERON:0005291!6.84e-15!604;UBERON:0006598!6.84e-15!604;UBERON:0002532!6.84e-15!604;UBERON:0002050!1.03e-14!605;UBERON:0005423!1.03e-14!605;UBERON:0000480!1.04e-14!626;UBERON:0004111!2.31e-14!241;UBERON:0000467!2.66e-14!625;UBERON:0000922!1.18e-13!612;UBERON:0004121!7.10e-13!169;UBERON:0000477!8.06e-13!286;UBERON:0000025!8.09e-13!194;UBERON:0002619!3.98e-12!22;UBERON:0000956!7.56e-12!25;UBERON:0000203!7.56e-12!25;UBERON:0000924!2.27e-11!173;UBERON:0006601!2.27e-11!173;UBERON:0000483!2.66e-11!309;UBERON:0000119!2.96e-11!312;UBERON:0000468!3.68e-11!659;UBERON:0001950!3.97e-11!20;UBERON:0000475!3.10e-10!365;UBERON:0000481!1.02e-09!347;UBERON:0000479!7.85e-09!787;UBERON:0002405!2.38e-07!115;UBERON:0002308!3.45e-07!9;UBERON:0000125!3.45e-07!9;UBERON:0002420!5.58e-07!9;UBERON:0007245!5.58e-07!9;UBERON:0010009!5.58e-07!9;UBERON:0010011!5.58e-07!9;UBERON:0000454!5.58e-07!9;UBERON:0003076!7.12e-07!15;UBERON:0003057!7.12e-07!15;UBERON:0002390!8.61e-07!102;UBERON:0003061!8.61e-07!102
|ontology_enrichment_uberon=UBERON:0007023!3.20e-36!114;UBERON:0001049!9.33e-27!56;UBERON:0005068!9.33e-27!56;UBERON:0006241!9.33e-27!56;UBERON:0007135!9.33e-27!56;UBERON:0000073!7.28e-25!53;UBERON:0002616!7.28e-25!53;UBERON:0003075!7.14e-23!82;UBERON:0007284!7.14e-23!82;UBERON:0000955!1.48e-22!68;UBERON:0006238!1.48e-22!68;UBERON:0001017!1.14e-21!81;UBERON:0002780!1.98e-21!41;UBERON:0001890!1.98e-21!41;UBERON:0003080!1.98e-21!41;UBERON:0006240!1.98e-21!41;UBERON:0001016!1.17e-19!89;UBERON:0002346!1.20e-19!86;UBERON:0003528!9.43e-18!34;UBERON:0002020!9.43e-18!34;UBERON:0001893!1.06e-17!34;UBERON:0003056!1.16e-17!61;UBERON:0002791!1.90e-16!32;UBERON:0001869!2.29e-16!32;UBERON:0010371!6.51e-16!104;UBERON:0010314!1.01e-15!132;UBERON:0000062!2.67e-15!503;UBERON:0000480!5.19e-14!625;UBERON:0000467!1.30e-13!624;UBERON:0004111!3.54e-13!240;UBERON:0011216!4.36e-13!223;UBERON:0000922!7.59e-13!592;UBERON:0005423!1.68e-12!581;UBERON:0002619!3.39e-12!22;UBERON:0000956!3.82e-12!25;UBERON:0000203!3.82e-12!25;UBERON:0000025!5.09e-12!192;UBERON:0004121!1.01e-11!171;UBERON:0000924!1.01e-11!171;UBERON:0006601!1.01e-11!171;UBERON:0000923!1.59e-11!560;UBERON:0010316!1.59e-11!560;UBERON:0005291!1.59e-11!560;UBERON:0006598!1.59e-11!560;UBERON:0010317!1.59e-11!560;UBERON:0002532!1.59e-11!560;UBERON:0001950!4.82e-11!20;UBERON:0000477!6.48e-11!373;UBERON:0002050!6.91e-11!564;UBERON:0000483!1.29e-10!306;UBERON:0000468!1.57e-10!656;UBERON:0000119!2.23e-10!309;UBERON:0000481!4.73e-10!342;UBERON:0000479!1.31e-08!773;UBERON:0000125!3.00e-07!9;UBERON:0002308!3.00e-07!9;UBERON:0002420!4.60e-07!9;UBERON:0007245!4.60e-07!9;UBERON:0010009!4.60e-07!9;UBERON:0010011!4.60e-07!9;UBERON:0000454!4.60e-07!9
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322392261994785!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464836051446145!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109173664096476!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000606382205165138!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310154483638162!REST#5978;3:9.65002871612802:0.00111263624711459:0.00771085713420044!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376369465757404!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331148688894232!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140886316298729
|tf_chipseq_enrich=EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322392261994785!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0464836051446145!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109173664096476!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000606382205165138!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00310154483638162!REST#5978;3:9.65002871612802:0.00111263624711459:0.00771085713420044!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376369465757404!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0331148688894232!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140886316298729
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}}
}}

Revision as of 16:07, 19 October 2012


Full id: C4657_corpus_globus_optic_thalamus_medulla_locus_substantia



Phase1 CAGE Peaks

Hg19::chr7:139477500..139477580,-p2@HIPK2
Hg19::chr7:139477785..139477853,-p1@HIPK2
Hg19::chr7:139477913..139477929,-p3@HIPK2


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>

Cell Type
Ontology termp-valuen
classical monocyte8.17e-1042
CD14-positive, CD16-negative classical monocyte8.17e-1042
defensive cell1.20e-0748
phagocyte1.20e-0748
myeloid leukocyte2.60e-0772
Uber Anatomy
Ontology termp-valuen
adult organism3.20e-36114
neural tube9.33e-2756
neural rod9.33e-2756
future spinal cord9.33e-2756
neural keel9.33e-2756
regional part of nervous system7.28e-2553
regional part of brain7.28e-2553
neural plate7.14e-2382
presumptive neural plate7.14e-2382
brain1.48e-2268
future brain1.48e-2268
central nervous system1.14e-2181
regional part of forebrain1.98e-2141
forebrain1.98e-2141
anterior neural tube1.98e-2141
future forebrain1.98e-2141
nervous system1.17e-1989
neurectoderm1.20e-1986
brain grey matter9.43e-1834
gray matter9.43e-1834
telencephalon1.06e-1734
pre-chordal neural plate1.16e-1761
regional part of telencephalon1.90e-1632
cerebral hemisphere2.29e-1632
ecto-epithelium6.51e-16104
structure with developmental contribution from neural crest1.01e-15132
organ2.67e-15503
anatomical group5.19e-14625
anatomical system1.30e-13624
anatomical conduit3.54e-13240
organ system subdivision4.36e-13223
embryo7.59e-13592
developing anatomical structure1.68e-12581
regional part of cerebral cortex3.39e-1222
cerebral cortex3.82e-1225
pallium3.82e-1225
tube5.09e-12192
ectoderm-derived structure1.01e-11171
ectoderm1.01e-11171
presumptive ectoderm1.01e-11171
germ layer1.59e-11560
germ layer / neural crest1.59e-11560
embryonic tissue1.59e-11560
presumptive structure1.59e-11560
germ layer / neural crest derived structure1.59e-11560
epiblast (generic)1.59e-11560
neocortex4.82e-1120
anatomical cluster6.48e-11373
embryonic structure6.91e-11564
epithelium1.29e-10306
multi-cellular organism1.57e-10656
cell layer2.23e-10309
multi-tissue structure4.73e-10342
tissue1.31e-08773
neural nucleus3.00e-079
nucleus of brain3.00e-079
basal ganglion4.60e-079
nuclear complex of neuraxis4.60e-079
aggregate regional part of brain4.60e-079
collection of basal ganglia4.60e-079
cerebral subcortex4.60e-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
EGR1#195834.988179094810140.008056488137383440.0322392261994785
ELF1#199734.258097958807540.01295179875054610.0464836051446145
HMGN3#932438.178547723350590.001827766942164210.0109173664096476
NR2C2#7182332.61461090524092.88098172333076e-050.000606382205165138
NR3C1#2908314.9730233311730.0002978331194675480.00310154483638162
REST#597839.650028716128020.001112636247114590.00771085713420044
SRF#6722313.79717826216780.0003806615025800190.00376369465757404
YY1#752834.911170749853860.008441455341808260.0331148688894232
ZBTB7A#5134137.35190930787590.002516255860282270.0140886316298729



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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