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Coexpression cluster:C2537: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!1.08e-24!86;UBERON:0001017!2.28e-24!82;UBERON:0000073!4.56e-24!94;UBERON:0001016!4.56e-24!94;UBERON:0007023!1.17e-22!115;UBERON:0002346!1.06e-21!90;UBERON:0003075!1.80e-20!86;UBERON:0007284!1.80e-20!86;UBERON:0000924!9.98e-19!173;UBERON:0006601!9.98e-19!173;UBERON:0000955!2.05e-18!69;UBERON:0006238!2.05e-18!69;UBERON:0001049!7.88e-18!57;UBERON:0005068!7.88e-18!57;UBERON:0006241!7.88e-18!57;UBERON:0007135!7.88e-18!57;UBERON:0004121!1.28e-17!169;UBERON:0000481!2.71e-17!347;UBERON:0000475!3.03e-17!365;UBERON:0002616!5.22e-17!59;UBERON:0000468!1.10e-15!659;UBERON:0003056!2.68e-15!61;UBERON:0000033!3.21e-14!123;UBERON:0000153!3.48e-14!129;UBERON:0007811!3.48e-14!129;UBERON:0003080!3.98e-14!42;UBERON:0002780!7.77e-14!41;UBERON:0001890!7.77e-14!41;UBERON:0006240!7.77e-14!41;UBERON:0000477!2.81e-13!286;UBERON:0001893!4.95e-13!34;UBERON:0001869!5.98e-13!32;UBERON:0000119!8.20e-13!312;UBERON:0000483!1.31e-12!309;UBERON:0002791!1.32e-12!33;UBERON:0002020!1.36e-12!34;UBERON:0003528!1.36e-12!34;UBERON:0000956!2.64e-11!25;UBERON:0000203!2.64e-11!25;UBERON:0000064!2.98e-11!219;UBERON:0000922!4.73e-11!612;UBERON:0004111!1.82e-10!241;UBERON:0000062!1.94e-10!511;UBERON:0000467!3.96e-10!625;UBERON:0000480!4.53e-10!626;UBERON:0002619!6.15e-10!22;UBERON:0000025!1.50e-09!194;UBERON:0001950!2.77e-09!20;UBERON:0002050!7.41e-09!605;UBERON:0005423!7.41e-09!605;UBERON:0000923!1.59e-08!604;UBERON:0005291!1.59e-08!604;UBERON:0006598!1.59e-08!604;UBERON:0002532!1.59e-08!604
|ontology_enrichment_uberon=UBERON:0005743!1.08e-24!86;UBERON:0001017!2.28e-24!82;UBERON:0000073!4.56e-24!94;UBERON:0001016!4.56e-24!94;UBERON:0007023!1.17e-22!115;UBERON:0002346!1.06e-21!90;UBERON:0003075!1.80e-20!86;UBERON:0007284!1.80e-20!86;UBERON:0000924!9.98e-19!173;UBERON:0006601!9.98e-19!173;UBERON:0000955!2.05e-18!69;UBERON:0006238!2.05e-18!69;UBERON:0001049!7.88e-18!57;UBERON:0005068!7.88e-18!57;UBERON:0006241!7.88e-18!57;UBERON:0007135!7.88e-18!57;UBERON:0004121!1.28e-17!169;UBERON:0000481!2.71e-17!347;UBERON:0000475!3.03e-17!365;UBERON:0002616!5.22e-17!59;UBERON:0000468!1.10e-15!659;UBERON:0003056!2.68e-15!61;UBERON:0000033!3.21e-14!123;UBERON:0000153!3.48e-14!129;UBERON:0007811!3.48e-14!129;UBERON:0003080!3.98e-14!42;UBERON:0002780!7.77e-14!41;UBERON:0001890!7.77e-14!41;UBERON:0006240!7.77e-14!41;UBERON:0000477!2.81e-13!286;UBERON:0001893!4.95e-13!34;UBERON:0001869!5.98e-13!32;UBERON:0000119!8.20e-13!312;UBERON:0000483!1.31e-12!309;UBERON:0002791!1.32e-12!33;UBERON:0002020!1.36e-12!34;UBERON:0003528!1.36e-12!34;UBERON:0000956!2.64e-11!25;UBERON:0000203!2.64e-11!25;UBERON:0000064!2.98e-11!219;UBERON:0000922!4.73e-11!612;UBERON:0004111!1.82e-10!241;UBERON:0000062!1.94e-10!511;UBERON:0000467!3.96e-10!625;UBERON:0000480!4.53e-10!626;UBERON:0002619!6.15e-10!22;UBERON:0000025!1.50e-09!194;UBERON:0001950!2.77e-09!20;UBERON:0002050!7.41e-09!605;UBERON:0005423!7.41e-09!605;UBERON:0000923!1.59e-08!604;UBERON:0005291!1.59e-08!604;UBERON:0006598!1.59e-08!604;UBERON:0002532!1.59e-08!604
|tf_chipseq_enrich=FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.0150374279649714
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}}
}}

Revision as of 12:00, 5 September 2012


Full id: C2537_uterus_occipital_cervix_rectum_mesothelioma_Cardiac_parietal



Phase1 CAGE Peaks

Hg19::chr1:164528911..164528940,+p7@PBX1
Hg19::chr1:164528942..164528964,+p11@PBX1
Hg19::chr1:164528975..164528998,+p13@PBX1
Hg19::chr1:164529004..164529015,+p15@PBX1


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
non-terminally differentiated cell6.03e-07180
Uber Anatomy
Ontology termp-valuen
central nervous system2.28e-2482
regional part of nervous system4.56e-2494
nervous system4.56e-2494
adult organism1.17e-22115
neurectoderm1.06e-2190
neural plate1.80e-2086
presumptive neural plate1.80e-2086
ectoderm9.98e-19173
presumptive ectoderm9.98e-19173
brain2.05e-1869
future brain2.05e-1869
neural tube7.88e-1857
neural rod7.88e-1857
future spinal cord7.88e-1857
neural keel7.88e-1857
ectoderm-derived structure1.28e-17169
multi-tissue structure2.71e-17347
organism subdivision3.03e-17365
regional part of brain5.22e-1759
multi-cellular organism1.10e-15659
pre-chordal neural plate2.68e-1561
head3.21e-14123
anterior region of body3.48e-14129
craniocervical region3.48e-14129
anterior neural tube3.98e-1442
regional part of forebrain7.77e-1441
forebrain7.77e-1441
future forebrain7.77e-1441
anatomical cluster2.81e-13286
telencephalon4.95e-1334
cerebral hemisphere5.98e-1332
cell layer8.20e-13312
epithelium1.31e-12309
regional part of telencephalon1.32e-1233
gray matter1.36e-1234
brain grey matter1.36e-1234
cerebral cortex2.64e-1125
pallium2.64e-1125
organ part2.98e-11219
embryo4.73e-11612
anatomical conduit1.82e-10241
organ1.94e-10511
anatomical system3.96e-10625
anatomical group4.53e-10626
regional part of cerebral cortex6.15e-1022
tube1.50e-09194
neocortex2.77e-0920
embryonic structure7.41e-09605
developing anatomical structure7.41e-09605
germ layer1.59e-08604
embryonic tissue1.59e-08604
presumptive structure1.59e-08604
epiblast (generic)1.59e-08604


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
FOXA1#316938.311064812039090.002740138182109850.0150374279649714



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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