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Coexpression cluster:C1664: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.78e-48!115;UBERON:0001049!5.04e-24!57;UBERON:0005068!5.04e-24!57;UBERON:0006241!5.04e-24!57;UBERON:0007135!5.04e-24!57;UBERON:0002616!3.21e-22!59;UBERON:0000955!7.34e-21!69;UBERON:0006238!7.34e-21!69;UBERON:0005743!1.09e-20!86;UBERON:0001017!1.09e-20!82;UBERON:0003075!3.52e-20!86;UBERON:0007284!3.52e-20!86;UBERON:0000073!1.06e-19!94;UBERON:0001016!1.06e-19!94;UBERON:0002346!3.04e-19!90;UBERON:0000481!1.21e-18!347;UBERON:0003080!1.52e-18!42;UBERON:0002780!7.86e-18!41;UBERON:0001890!7.86e-18!41;UBERON:0006240!7.86e-18!41;UBERON:0002020!1.74e-15!34;UBERON:0003528!1.74e-15!34;UBERON:0000064!1.93e-15!219;UBERON:0001893!2.11e-15!34;UBERON:0000475!3.75e-15!365;UBERON:0001869!5.72e-15!32;UBERON:0002791!7.81e-15!33;UBERON:0000153!1.01e-14!129;UBERON:0007811!1.01e-14!129;UBERON:0000033!3.41e-14!123;UBERON:0003056!7.29e-14!61;UBERON:0000477!2.33e-13!286;UBERON:0002619!4.26e-13!22;UBERON:0000062!5.73e-13!511;UBERON:0001950!4.15e-12!20;UBERON:0004121!4.48e-12!169;UBERON:0000924!9.06e-12!173;UBERON:0006601!9.06e-12!173;UBERON:0000468!1.63e-11!659;UBERON:0000956!6.38e-11!25;UBERON:0000203!6.38e-11!25;UBERON:0000922!8.32e-10!612;UBERON:0004111!2.10e-09!241;UBERON:0000025!2.24e-09!194;UBERON:0009569!2.66e-09!113;UBERON:0000063!4.21e-09!97;UBERON:0000466!8.72e-09!126;UBERON:0002050!8.95e-09!605;UBERON:0005423!8.95e-09!605;UBERON:0000464!1.50e-08!104;UBERON:0000923!1.99e-08!604;UBERON:0005291!1.99e-08!604;UBERON:0006598!1.99e-08!604;UBERON:0002532!1.99e-08!604;UBERON:0000483!4.37e-08!309;UBERON:0000119!4.63e-08!312;UBERON:0000467!1.13e-07!625;UBERON:0000480!1.55e-07!626;UBERON:0002553!1.91e-07!70;UBERON:0004921!2.22e-07!129;UBERON:0004185!2.22e-07!129;UBERON:0001048!9.64e-07!168
|ontology_enrichment_uberon=UBERON:0007023!8.78e-48!115;UBERON:0001049!5.04e-24!57;UBERON:0005068!5.04e-24!57;UBERON:0006241!5.04e-24!57;UBERON:0007135!5.04e-24!57;UBERON:0002616!3.21e-22!59;UBERON:0000955!7.34e-21!69;UBERON:0006238!7.34e-21!69;UBERON:0005743!1.09e-20!86;UBERON:0001017!1.09e-20!82;UBERON:0003075!3.52e-20!86;UBERON:0007284!3.52e-20!86;UBERON:0000073!1.06e-19!94;UBERON:0001016!1.06e-19!94;UBERON:0002346!3.04e-19!90;UBERON:0000481!1.21e-18!347;UBERON:0003080!1.52e-18!42;UBERON:0002780!7.86e-18!41;UBERON:0001890!7.86e-18!41;UBERON:0006240!7.86e-18!41;UBERON:0002020!1.74e-15!34;UBERON:0003528!1.74e-15!34;UBERON:0000064!1.93e-15!219;UBERON:0001893!2.11e-15!34;UBERON:0000475!3.75e-15!365;UBERON:0001869!5.72e-15!32;UBERON:0002791!7.81e-15!33;UBERON:0000153!1.01e-14!129;UBERON:0007811!1.01e-14!129;UBERON:0000033!3.41e-14!123;UBERON:0003056!7.29e-14!61;UBERON:0000477!2.33e-13!286;UBERON:0002619!4.26e-13!22;UBERON:0000062!5.73e-13!511;UBERON:0001950!4.15e-12!20;UBERON:0004121!4.48e-12!169;UBERON:0000924!9.06e-12!173;UBERON:0006601!9.06e-12!173;UBERON:0000468!1.63e-11!659;UBERON:0000956!6.38e-11!25;UBERON:0000203!6.38e-11!25;UBERON:0000922!8.32e-10!612;UBERON:0004111!2.10e-09!241;UBERON:0000025!2.24e-09!194;UBERON:0009569!2.66e-09!113;UBERON:0000063!4.21e-09!97;UBERON:0000466!8.72e-09!126;UBERON:0002050!8.95e-09!605;UBERON:0005423!8.95e-09!605;UBERON:0000464!1.50e-08!104;UBERON:0000923!1.99e-08!604;UBERON:0005291!1.99e-08!604;UBERON:0006598!1.99e-08!604;UBERON:0002532!1.99e-08!604;UBERON:0000483!4.37e-08!309;UBERON:0000119!4.63e-08!312;UBERON:0000467!1.13e-07!625;UBERON:0000480!1.55e-07!626;UBERON:0002553!1.91e-07!70;UBERON:0004921!2.22e-07!129;UBERON:0004185!2.22e-07!129;UBERON:0001048!9.64e-07!168
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}}
}}

Revision as of 14:13, 5 September 2012


Full id: C1664_uterus_epididymis_aorta_cervix_caudate_Adipocyte_ductus



Phase1 CAGE Peaks

Hg19::chr12:15374234..15374247,-p3@RERG
Hg19::chr12:15374258..15374265,-p5@RERG
Hg19::chr12:15374283..15374294,-p4@RERG
Hg19::chr12:15374328..15374342,-p2@RERG
Hg19::chr12:15374343..15374416,-p1@RERG


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
adult organism8.78e-48115
neural tube5.04e-2457
neural rod5.04e-2457
future spinal cord5.04e-2457
neural keel5.04e-2457
regional part of brain3.21e-2259
brain7.34e-2169
future brain7.34e-2169
central nervous system1.09e-2082
neural plate3.52e-2086
presumptive neural plate3.52e-2086
regional part of nervous system1.06e-1994
nervous system1.06e-1994
neurectoderm3.04e-1990
multi-tissue structure1.21e-18347
anterior neural tube1.52e-1842
regional part of forebrain7.86e-1841
forebrain7.86e-1841
future forebrain7.86e-1841
gray matter1.74e-1534
brain grey matter1.74e-1534
organ part1.93e-15219
telencephalon2.11e-1534
organism subdivision3.75e-15365
cerebral hemisphere5.72e-1532
regional part of telencephalon7.81e-1533
anterior region of body1.01e-14129
craniocervical region1.01e-14129
head3.41e-14123
pre-chordal neural plate7.29e-1461
anatomical cluster2.33e-13286
regional part of cerebral cortex4.26e-1322
organ5.73e-13511
neocortex4.15e-1220
ectoderm-derived structure4.48e-12169
ectoderm9.06e-12173
presumptive ectoderm9.06e-12173
multi-cellular organism1.63e-11659
cerebral cortex6.38e-1125
pallium6.38e-1125
embryo8.32e-10612
anatomical conduit2.10e-09241
tube2.24e-09194
subdivision of trunk2.66e-09113
organ segment4.21e-0997
immaterial anatomical entity8.72e-09126
embryonic structure8.95e-09605
developing anatomical structure8.95e-09605
anatomical space1.50e-08104
germ layer1.99e-08604
embryonic tissue1.99e-08604
presumptive structure1.99e-08604
epiblast (generic)1.99e-08604
epithelium4.37e-08309
cell layer4.63e-08312
anatomical system1.13e-07625
anatomical group1.55e-07626
anatomical cavity1.91e-0770
subdivision of digestive tract2.22e-07129
endodermal part of digestive tract2.22e-07129
primordium9.64e-07168


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
CTCF#1066455.360256373075030.0002259278299937090.00249531267308724
CTCFL#140690519.74647435897443.32745051287657e-071.65641374697005e-05
MAX#414956.452555509007128.93743970843928e-050.00130584396433924
MYC#460944.177825497287520.005691969036823440.0256710089492077
NFKB1#479055.488063424193840.0002008162847462320.00238818628588154
PAX5#507956.669565531177837.57493746384605e-050.00116942925910808
RAD21#5885510.35503389545638.39503550283973e-060.000229340599759633
SMC3#9126515.04493284493281.29633924985553e-065.15568830600387e-05
SPI1#668858.204323508522732.68916109982495e-050.000574107310107559
ZNF143#7702513.50087655222792.22790360787208e-067.97395561694831e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000570699754967525



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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