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Coexpression cluster:C4735: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!5.24e-27!659;UBERON:0000467!4.68e-23!625;UBERON:0000480!8.21e-23!626;UBERON:0000475!2.47e-20!365;UBERON:0000922!5.30e-18!612;UBERON:0005743!6.61e-18!86;UBERON:0001017!2.05e-17!82;UBERON:0000119!3.16e-17!312;UBERON:0000477!3.93e-17!286;UBERON:0002616!6.13e-17!59;UBERON:0000483!6.61e-17!309;UBERON:0001049!1.30e-16!57;UBERON:0005068!1.30e-16!57;UBERON:0006241!1.30e-16!57;UBERON:0007135!1.30e-16!57;UBERON:0000025!1.39e-16!194;UBERON:0002050!2.28e-16!605;UBERON:0005423!2.28e-16!605;UBERON:0000923!5.42e-16!604;UBERON:0005291!5.42e-16!604;UBERON:0006598!5.42e-16!604;UBERON:0002532!5.42e-16!604;UBERON:0004111!5.89e-16!241;UBERON:0000062!8.40e-16!511;UBERON:0000955!9.60e-16!69;UBERON:0006238!9.60e-16!69;UBERON:0003075!1.05e-15!86;UBERON:0007284!1.05e-15!86;UBERON:0000073!3.16e-15!94;UBERON:0001016!3.16e-15!94;UBERON:0000481!3.33e-13!347;UBERON:0002346!4.59e-13!90;UBERON:0007023!5.43e-12!115;UBERON:0000033!8.24e-12!123;UBERON:0004121!1.60e-11!169;UBERON:0002020!1.99e-10!34;UBERON:0003528!1.99e-10!34;UBERON:0000153!2.16e-10!129;UBERON:0007811!2.16e-10!129;UBERON:0003056!3.88e-10!61;UBERON:0001893!4.53e-10!34;UBERON:0003080!5.42e-10!42;UBERON:0000924!5.45e-10!173;UBERON:0006601!5.45e-10!173;UBERON:0002791!5.49e-10!33;UBERON:0002780!9.76e-10!41;UBERON:0001890!9.76e-10!41;UBERON:0006240!9.76e-10!41;UBERON:0000064!2.35e-09!219;UBERON:0002100!2.77e-09!216;UBERON:0001869!4.42e-09!32;UBERON:0003076!1.45e-08!15;UBERON:0003057!1.45e-08!15;UBERON:0005256!4.50e-08!143;UBERON:0000956!1.48e-07!25;UBERON:0000203!1.48e-07!25;UBERON:0002619!2.40e-07!22;UBERON:0004733!9.39e-07!12;UBERON:0002028!9.39e-07!12;UBERON:0007277!9.39e-07!12
|ontology_enrichment_uberon=UBERON:0000468!5.24e-27!659;UBERON:0000467!4.68e-23!625;UBERON:0000480!8.21e-23!626;UBERON:0000475!2.47e-20!365;UBERON:0000922!5.30e-18!612;UBERON:0005743!6.61e-18!86;UBERON:0001017!2.05e-17!82;UBERON:0000119!3.16e-17!312;UBERON:0000477!3.93e-17!286;UBERON:0002616!6.13e-17!59;UBERON:0000483!6.61e-17!309;UBERON:0001049!1.30e-16!57;UBERON:0005068!1.30e-16!57;UBERON:0006241!1.30e-16!57;UBERON:0007135!1.30e-16!57;UBERON:0000025!1.39e-16!194;UBERON:0002050!2.28e-16!605;UBERON:0005423!2.28e-16!605;UBERON:0000923!5.42e-16!604;UBERON:0005291!5.42e-16!604;UBERON:0006598!5.42e-16!604;UBERON:0002532!5.42e-16!604;UBERON:0004111!5.89e-16!241;UBERON:0000062!8.40e-16!511;UBERON:0000955!9.60e-16!69;UBERON:0006238!9.60e-16!69;UBERON:0003075!1.05e-15!86;UBERON:0007284!1.05e-15!86;UBERON:0000073!3.16e-15!94;UBERON:0001016!3.16e-15!94;UBERON:0000481!3.33e-13!347;UBERON:0002346!4.59e-13!90;UBERON:0007023!5.43e-12!115;UBERON:0000033!8.24e-12!123;UBERON:0004121!1.60e-11!169;UBERON:0002020!1.99e-10!34;UBERON:0003528!1.99e-10!34;UBERON:0000153!2.16e-10!129;UBERON:0007811!2.16e-10!129;UBERON:0003056!3.88e-10!61;UBERON:0001893!4.53e-10!34;UBERON:0003080!5.42e-10!42;UBERON:0000924!5.45e-10!173;UBERON:0006601!5.45e-10!173;UBERON:0002791!5.49e-10!33;UBERON:0002780!9.76e-10!41;UBERON:0001890!9.76e-10!41;UBERON:0006240!9.76e-10!41;UBERON:0000064!2.35e-09!219;UBERON:0002100!2.77e-09!216;UBERON:0001869!4.42e-09!32;UBERON:0003076!1.45e-08!15;UBERON:0003057!1.45e-08!15;UBERON:0005256!4.50e-08!143;UBERON:0000956!1.48e-07!25;UBERON:0000203!1.48e-07!25;UBERON:0002619!2.40e-07!22;UBERON:0004733!9.39e-07!12;UBERON:0002028!9.39e-07!12;UBERON:0007277!9.39e-07!12
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}}
}}

Revision as of 20:17, 8 August 2012


Full id: C4735_Mesenchymal_Pericytes_spinal_Astrocyte_hippocampus_Osteoblast_MCF7



Phase1 CAGE Peaks

Hg19::chr8:145027973..145027992,-p11@PLEC
Hg19::chr8:145027995..145028012,-p9@PLEC
Hg19::chr8:145028013..145028035,-p13@PLEC


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 cell1.86e-10180
Uber Anatomy
Ontology termp-valuen
multi-cellular organism5.24e-27659
anatomical system4.68e-23625
anatomical group8.21e-23626
organism subdivision2.47e-20365
embryo5.30e-18612
central nervous system2.05e-1782
cell layer3.16e-17312
anatomical cluster3.93e-17286
regional part of brain6.13e-1759
epithelium6.61e-17309
neural tube1.30e-1657
neural rod1.30e-1657
future spinal cord1.30e-1657
neural keel1.30e-1657
tube1.39e-16194
embryonic structure2.28e-16605
developing anatomical structure2.28e-16605
germ layer5.42e-16604
embryonic tissue5.42e-16604
presumptive structure5.42e-16604
epiblast (generic)5.42e-16604
anatomical conduit5.89e-16241
organ8.40e-16511
brain9.60e-1669
future brain9.60e-1669
neural plate1.05e-1586
presumptive neural plate1.05e-1586
regional part of nervous system3.16e-1594
nervous system3.16e-1594
multi-tissue structure3.33e-13347
neurectoderm4.59e-1390
adult organism5.43e-12115
head8.24e-12123
ectoderm-derived structure1.60e-11169
gray matter1.99e-1034
brain grey matter1.99e-1034
anterior region of body2.16e-10129
craniocervical region2.16e-10129
pre-chordal neural plate3.88e-1061
telencephalon4.53e-1034
anterior neural tube5.42e-1042
ectoderm5.45e-10173
presumptive ectoderm5.45e-10173
regional part of telencephalon5.49e-1033
regional part of forebrain9.76e-1041
forebrain9.76e-1041
future forebrain9.76e-1041
organ part2.35e-09219
trunk2.77e-09216
cerebral hemisphere4.42e-0932
posterior neural tube1.45e-0815
chordal neural plate1.45e-0815
trunk mesenchyme4.50e-08143
cerebral cortex1.48e-0725
pallium1.48e-0725
regional part of cerebral cortex2.40e-0722
segmental subdivision of hindbrain9.39e-0712
hindbrain9.39e-0712
presumptive hindbrain9.39e-0712


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


No analysis results for this cluster

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.