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Coexpression cluster:C2566: Difference between revisions

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|full_id=C2566_Lens_gall_papillotubular_anaplastic_Ciliary_osteoclastoma_alveolar
|full_id=C2566_Lens_gall_papillotubular_anaplastic_Ciliary_osteoclastoma_alveolar
|id=C2566
|id=C2566
|ontology_enrichment_celltype=CL:0000359!8.39e-08!32
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000477!4.54e-28!286;UBERON:0000119!1.03e-27!312;UBERON:0000483!2.09e-26!309;UBERON:0004111!8.92e-26!241;UBERON:0000481!1.01e-25!347;UBERON:0000033!5.12e-24!123;UBERON:0000475!1.92e-23!365;UBERON:0000153!4.55e-22!129;UBERON:0007811!4.55e-22!129;UBERON:0000025!1.02e-21!194;UBERON:0004121!4.04e-21!169;UBERON:0003075!7.02e-21!86;UBERON:0007284!7.02e-21!86;UBERON:0000924!1.13e-20!173;UBERON:0006601!1.13e-20!173;UBERON:0005743!1.39e-20!86;UBERON:0000468!3.01e-20!659;UBERON:0002346!5.50e-20!90;UBERON:0001017!9.67e-20!82;UBERON:0000955!1.13e-19!69;UBERON:0006238!1.13e-19!69;UBERON:0000073!3.58e-19!94;UBERON:0001016!3.58e-19!94;UBERON:0000467!3.22e-18!625;UBERON:0002616!5.11e-18!59;UBERON:0002050!5.56e-18!605;UBERON:0005423!5.56e-18!605;UBERON:0000480!6.31e-18!626;UBERON:0000922!7.25e-18!612;UBERON:0000923!9.18e-18!604;UBERON:0005291!9.18e-18!604;UBERON:0006598!9.18e-18!604;UBERON:0002532!9.18e-18!604;UBERON:0001049!1.12e-16!57;UBERON:0005068!1.12e-16!57;UBERON:0006241!1.12e-16!57;UBERON:0007135!1.12e-16!57;UBERON:0003056!2.70e-15!61;UBERON:0000062!5.68e-15!511;UBERON:0002780!1.69e-12!41;UBERON:0001890!1.69e-12!41;UBERON:0006240!1.69e-12!41;UBERON:0003080!3.13e-12!42;UBERON:0000064!8.35e-12!219;UBERON:0002020!9.17e-12!34;UBERON:0003528!9.17e-12!34;UBERON:0001893!1.61e-11!34;UBERON:0002791!2.25e-11!33;UBERON:0001869!5.28e-11!32;UBERON:0000956!3.20e-09!25;UBERON:0000203!3.20e-09!25;UBERON:0003914!8.49e-09!118;UBERON:0002049!8.56e-09!79;UBERON:0007798!8.56e-09!79;UBERON:0005256!1.14e-08!143;UBERON:0002619!1.09e-07!22;UBERON:0002100!1.91e-07!216;UBERON:0000058!2.71e-07!26;UBERON:0003104!2.94e-07!238;UBERON:0009142!2.94e-07!238;UBERON:0007023!3.37e-07!115;UBERON:0001950!6.23e-07!20
|ontology_enrichment_uberon=UBERON:0000477!3.12e-24!373;UBERON:0000119!1.17e-20!309;UBERON:0004111!3.70e-20!240;UBERON:0000483!2.68e-19!306;UBERON:0000025!2.37e-18!192;UBERON:0000481!9.08e-18!342;UBERON:0010314!9.19e-18!132;UBERON:0000955!1.59e-17!68;UBERON:0006238!1.59e-17!68;UBERON:0001017!2.45e-17!81;UBERON:0003075!5.88e-17!82;UBERON:0007284!5.88e-17!82;UBERON:0002346!1.50e-16!86;UBERON:0001016!2.00e-15!89;UBERON:0004121!1.46e-14!171;UBERON:0000924!1.46e-14!171;UBERON:0006601!1.46e-14!171;UBERON:0010371!2.57e-14!104;UBERON:0001049!6.28e-14!56;UBERON:0005068!6.28e-14!56;UBERON:0006241!6.28e-14!56;UBERON:0007135!6.28e-14!56;UBERON:0000073!2.56e-13!53;UBERON:0002616!2.56e-13!53;UBERON:0003056!8.63e-12!61;UBERON:0011216!2.55e-11!223;UBERON:0002780!2.18e-10!41;UBERON:0001890!2.18e-10!41;UBERON:0003080!2.18e-10!41;UBERON:0006240!2.18e-10!41;UBERON:0003528!7.51e-10!34;UBERON:0002020!7.51e-10!34;UBERON:0001893!7.73e-10!34;UBERON:0001869!2.61e-09!32;UBERON:0000922!2.68e-09!592;UBERON:0002791!3.71e-09!32;UBERON:0000468!9.35e-09!656;UBERON:0006876!2.46e-08!11;UBERON:0003914!3.76e-08!117;UBERON:0000467!4.86e-08!624;UBERON:0000480!6.32e-08!625;UBERON:0005423!7.23e-08!581;UBERON:0002050!8.45e-08!564;UBERON:0002049!2.60e-07!78;UBERON:0007798!2.60e-07!78;UBERON:0000923!3.02e-07!560;UBERON:0010316!3.02e-07!560;UBERON:0005291!3.02e-07!560;UBERON:0006598!3.02e-07!560;UBERON:0010317!3.02e-07!560;UBERON:0002532!3.02e-07!560;UBERON:0000956!4.82e-07!25;UBERON:0000203!4.82e-07!25;UBERON:0000064!9.47e-07!218
|tf_chipseq_enrich=CEBPB#1051;3:5.97836071936861:0.00715383248472697:0.0297309634250856!CTBP2#1488;4:62.7170003393281:6.45042639894877e-08:3.96047079764733e-06!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.0081770516848845!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997379767860863!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722312321616473!GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.77702049946094e-05!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466269454509658!TAL1#6886;4:29.8686166774402:1.25525650806991e-06:5.04222055562743e-05!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244431463808335!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483090612906808!USF2#7392;3:9.7441480388022:0.00171834184841007:0.0107218248480165!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249072463776004
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}}
}}

Revision as of 14:10, 19 October 2012


Full id: C2566_Lens_gall_papillotubular_anaplastic_Ciliary_osteoclastoma_alveolar



Phase1 CAGE Peaks

Hg19::chr1:218518669..218518689,+p1@TGFB2
Hg19::chr1:218518858..218518869,+p21@TGFB2
Hg19::chr1:218518942..218518953,+p28@TGFB2
Hg19::chr1:218519057..218519070,+p11@TGFB2


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
anatomical cluster3.12e-24373
cell layer1.17e-20309
anatomical conduit3.70e-20240
epithelium2.68e-19306
tube2.37e-18192
multi-tissue structure9.08e-18342
structure with developmental contribution from neural crest9.19e-18132
brain1.59e-1768
future brain1.59e-1768
central nervous system2.45e-1781
neural plate5.88e-1782
presumptive neural plate5.88e-1782
neurectoderm1.50e-1686
nervous system2.00e-1589
ectoderm-derived structure1.46e-14171
ectoderm1.46e-14171
presumptive ectoderm1.46e-14171
ecto-epithelium2.57e-14104
neural tube6.28e-1456
neural rod6.28e-1456
future spinal cord6.28e-1456
neural keel6.28e-1456
regional part of nervous system2.56e-1353
regional part of brain2.56e-1353
pre-chordal neural plate8.63e-1261
organ system subdivision2.55e-11223
regional part of forebrain2.18e-1041
forebrain2.18e-1041
anterior neural tube2.18e-1041
future forebrain2.18e-1041
brain grey matter7.51e-1034
gray matter7.51e-1034
telencephalon7.73e-1034
cerebral hemisphere2.61e-0932
embryo2.68e-09592
regional part of telencephalon3.71e-0932
multi-cellular organism9.35e-09656
vasculature of organ2.46e-0811
epithelial tube3.76e-08117
anatomical system4.86e-08624
anatomical group6.32e-08625
developing anatomical structure7.23e-08581
embryonic structure8.45e-08564
vasculature2.60e-0778
vascular system2.60e-0778
germ layer3.02e-07560
germ layer / neural crest3.02e-07560
embryonic tissue3.02e-07560
presumptive structure3.02e-07560
germ layer / neural crest derived structure3.02e-07560
epiblast (generic)3.02e-07560
cerebral cortex4.82e-0725
pallium4.82e-0725
organ part9.47e-07218


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
CEBPB#105135.978360719368610.007153832484726970.0297309634250856
CTBP2#1488462.71700033932816.45042639894877e-083.96047079764733e-06
CTCF#1066445.360256373075030.001211145381643620.0081770516848845
E2F6#187645.017155731697390.00157802193473060.00997379767860863
GATA2#2624412.7449317335543.78864877853583e-050.000722312321616473
GATA3#2625427.2365163572061.81561517799785e-066.77702049946094e-05
MAX#414934.839416631755340.01315737137836840.0466269454509658
TAL1#6886429.86861667744021.25525650806991e-065.04222055562743e-05
TBP#690843.706770687096390.005296377814784350.0244431463808335
USF1#739134.771124457905970.01370465887188020.0483090612906808
USF2#739239.74414803880220.001718341848410070.0107218248480165
ZNF263#1012748.221841637010680.0002187871180958320.00249072463776004



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.