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Coexpression cluster:C754: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!1.61e-29!94;UBERON:0001016!1.61e-29!94;UBERON:0005743!2.49e-29!86;UBERON:0001049!3.66e-29!57;UBERON:0005068!3.66e-29!57;UBERON:0006241!3.66e-29!57;UBERON:0007135!3.66e-29!57;UBERON:0001017!1.41e-28!82;UBERON:0007023!2.79e-26!115;UBERON:0003075!7.76e-24!86;UBERON:0007284!7.76e-24!86;UBERON:0002346!9.55e-24!90;UBERON:0002780!2.05e-23!41;UBERON:0001890!2.05e-23!41;UBERON:0006240!2.05e-23!41;UBERON:0003080!2.73e-23!42;UBERON:0002616!3.09e-23!59;UBERON:0000955!7.97e-23!69;UBERON:0006238!7.97e-23!69;UBERON:0000924!2.67e-22!173;UBERON:0006601!2.67e-22!173;UBERON:0004121!4.41e-22!169;UBERON:0002020!4.37e-21!34;UBERON:0003528!4.37e-21!34;UBERON:0001893!4.87e-21!34;UBERON:0002791!1.87e-20!33;UBERON:0001869!2.71e-20!32;UBERON:0000062!1.21e-19!511;UBERON:0000064!1.86e-18!219;UBERON:0003056!4.55e-18!61;UBERON:0000468!3.53e-17!659;UBERON:0000956!3.63e-16!25;UBERON:0000203!3.63e-16!25;UBERON:0000481!4.55e-16!347;UBERON:0000033!7.86e-16!123;UBERON:0000475!2.13e-15!365;UBERON:0000922!2.23e-15!612;UBERON:0002619!2.23e-14!22;UBERON:0000153!2.54e-14!129;UBERON:0007811!2.54e-14!129;UBERON:0000467!1.90e-13!625;UBERON:0001950!3.40e-13!20;UBERON:0000480!4.10e-13!626;UBERON:0002050!6.49e-13!605;UBERON:0005423!6.49e-13!605;UBERON:0000923!1.25e-12!604;UBERON:0005291!1.25e-12!604;UBERON:0006598!1.25e-12!604;UBERON:0002532!1.25e-12!604;UBERON:0000483!1.48e-08!309;UBERON:0000119!4.37e-08!312;UBERON:0003076!4.14e-07!15;UBERON:0003057!4.14e-07!15
|ontology_enrichment_uberon=UBERON:0000073!1.61e-29!94;UBERON:0001016!1.61e-29!94;UBERON:0005743!2.49e-29!86;UBERON:0001049!3.66e-29!57;UBERON:0005068!3.66e-29!57;UBERON:0006241!3.66e-29!57;UBERON:0007135!3.66e-29!57;UBERON:0001017!1.41e-28!82;UBERON:0007023!2.79e-26!115;UBERON:0003075!7.76e-24!86;UBERON:0007284!7.76e-24!86;UBERON:0002346!9.55e-24!90;UBERON:0002780!2.05e-23!41;UBERON:0001890!2.05e-23!41;UBERON:0006240!2.05e-23!41;UBERON:0003080!2.73e-23!42;UBERON:0002616!3.09e-23!59;UBERON:0000955!7.97e-23!69;UBERON:0006238!7.97e-23!69;UBERON:0000924!2.67e-22!173;UBERON:0006601!2.67e-22!173;UBERON:0004121!4.41e-22!169;UBERON:0002020!4.37e-21!34;UBERON:0003528!4.37e-21!34;UBERON:0001893!4.87e-21!34;UBERON:0002791!1.87e-20!33;UBERON:0001869!2.71e-20!32;UBERON:0000062!1.21e-19!511;UBERON:0000064!1.86e-18!219;UBERON:0003056!4.55e-18!61;UBERON:0000468!3.53e-17!659;UBERON:0000956!3.63e-16!25;UBERON:0000203!3.63e-16!25;UBERON:0000481!4.55e-16!347;UBERON:0000033!7.86e-16!123;UBERON:0000475!2.13e-15!365;UBERON:0000922!2.23e-15!612;UBERON:0002619!2.23e-14!22;UBERON:0000153!2.54e-14!129;UBERON:0007811!2.54e-14!129;UBERON:0000467!1.90e-13!625;UBERON:0001950!3.40e-13!20;UBERON:0000480!4.10e-13!626;UBERON:0002050!6.49e-13!605;UBERON:0005423!6.49e-13!605;UBERON:0000923!1.25e-12!604;UBERON:0005291!1.25e-12!604;UBERON:0006598!1.25e-12!604;UBERON:0002532!1.25e-12!604;UBERON:0000483!1.48e-08!309;UBERON:0000119!4.37e-08!312;UBERON:0003076!4.14e-07!15;UBERON:0003057!4.14e-07!15
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}}
}}

Revision as of 11:44, 5 September 2012


Full id: C754_occipital_temporal_pineal_postcentral_Alveolar_colon_parietal



Phase1 CAGE Peaks

Hg19::chr14:103987731..103987748,-p6@CKB
Hg19::chr14:103988257..103988300,-p10@CKB
Hg19::chr14:103988384..103988399,-p15@CKB
Hg19::chr14:103988406..103988482,-p4@CKB
Hg19::chr14:103988664..103988673,-p14@CKB
Hg19::chr14:103988694..103988705,-p13@CKB
Hg19::chr14:103988723..103988744,-p9@CKB
Hg19::chr14:103988768..103988787,-p2@CKB
Hg19::chr14:103988801..103988816,-p8@CKB
Hg19::chr14:103988826..103988852,-p5@CKB
Hg19::chr14:103989160..103989176,-p1@CKB


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
regional part of nervous system1.61e-2994
nervous system1.61e-2994
neural tube3.66e-2957
neural rod3.66e-2957
future spinal cord3.66e-2957
neural keel3.66e-2957
central nervous system1.41e-2882
adult organism2.79e-26115
neural plate7.76e-2486
presumptive neural plate7.76e-2486
neurectoderm9.55e-2490
regional part of forebrain2.05e-2341
forebrain2.05e-2341
future forebrain2.05e-2341
anterior neural tube2.73e-2342
regional part of brain3.09e-2359
brain7.97e-2369
future brain7.97e-2369
ectoderm2.67e-22173
presumptive ectoderm2.67e-22173
ectoderm-derived structure4.41e-22169
gray matter4.37e-2134
brain grey matter4.37e-2134
telencephalon4.87e-2134
regional part of telencephalon1.87e-2033
cerebral hemisphere2.71e-2032
organ1.21e-19511
organ part1.86e-18219
pre-chordal neural plate4.55e-1861
multi-cellular organism3.53e-17659
cerebral cortex3.63e-1625
pallium3.63e-1625
multi-tissue structure4.55e-16347
head7.86e-16123
organism subdivision2.13e-15365
embryo2.23e-15612
regional part of cerebral cortex2.23e-1422
anterior region of body2.54e-14129
craniocervical region2.54e-14129
anatomical system1.90e-13625
neocortex3.40e-1320
anatomical group4.10e-13626
embryonic structure6.49e-13605
developing anatomical structure6.49e-13605
germ layer1.25e-12604
embryonic tissue1.25e-12604
presumptive structure1.25e-12604
epiblast (generic)1.25e-12604
epithelium1.48e-08309
cell layer4.37e-08312
posterior neural tube4.14e-0715
chordal neural plate4.14e-0715


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#90595.184164926605792.45776684955985e-068.68064633078056e-05
E2F1#1869104.461262922617571.10540139252827e-064.58304946543312e-05
E2F6#1876115.017155731697391.96991453050942e-081.40818551438654e-06
ETS1#211365.306596866655820.0003440581432184970.00347414564629185
GTF2F1#296255.790754943980750.0009189250417807320.00668279454345365
POLR2A#5430112.147453176558070.0002231983422387430.00248513983636163
TAF7#687955.196849729510870.001505235623027780.00961441521823733
ZBTB7A#51341117.35190930787592.94291302586626e-102.98402809231502e-08



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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