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Coexpression cluster:C3386: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000119!1.63e-24!312;UBERON:0000483!2.31e-24!309;UBERON:0000475!1.49e-22!365;UBERON:0000025!3.03e-21!194;UBERON:0004111!3.49e-21!241;UBERON:0000481!7.72e-21!347;UBERON:0000477!4.56e-20!286;UBERON:0000468!4.54e-19!659;UBERON:0000467!3.51e-18!625;UBERON:0000480!8.41e-18!626;UBERON:0004121!3.41e-17!169;UBERON:0000922!8.80e-17!612;UBERON:0000924!1.45e-15!173;UBERON:0006601!1.45e-15!173;UBERON:0003075!1.53e-15!86;UBERON:0007284!1.53e-15!86;UBERON:0000033!8.98e-15!123;UBERON:0002050!1.12e-14!605;UBERON:0005423!1.12e-14!605;UBERON:0000923!1.81e-14!604;UBERON:0005291!1.81e-14!604;UBERON:0006598!1.81e-14!604;UBERON:0002532!1.81e-14!604;UBERON:0000914!2.15e-14!83;UBERON:0002329!2.15e-14!83;UBERON:0003077!2.15e-14!83;UBERON:0003059!2.15e-14!83;UBERON:0007282!2.15e-14!83;UBERON:0009618!2.15e-14!83;UBERON:0007285!2.15e-14!83;UBERON:0005743!1.46e-13!86;UBERON:0002346!2.42e-13!90;UBERON:0000153!3.64e-13!129;UBERON:0007811!3.64e-13!129;UBERON:0000073!5.33e-13!94;UBERON:0001016!5.33e-13!94;UBERON:0002049!5.61e-13!79;UBERON:0007798!5.61e-13!79;UBERON:0005256!9.45e-13!143;UBERON:0003914!2.23e-12!118;UBERON:0001049!3.01e-12!57;UBERON:0005068!3.01e-12!57;UBERON:0006241!3.01e-12!57;UBERON:0007135!3.01e-12!57;UBERON:0001637!4.79e-12!42;UBERON:0003509!4.79e-12!42;UBERON:0004572!4.79e-12!42;UBERON:0001017!6.22e-12!82;UBERON:0004290!1.15e-11!70;UBERON:0000055!1.80e-11!69;UBERON:0001981!7.57e-11!60;UBERON:0007500!7.57e-11!60;UBERON:0004537!7.57e-11!60;UBERON:0006965!7.57e-11!60;UBERON:0003056!1.52e-10!61;UBERON:0002616!2.71e-10!59;UBERON:0004872!2.97e-10!84;UBERON:0004573!7.64e-10!33;UBERON:0004571!7.64e-10!33;UBERON:0000486!2.69e-09!82;UBERON:0000955!2.89e-09!69;UBERON:0006238!2.89e-09!69;UBERON:0001134!9.91e-09!61;UBERON:0002036!9.91e-09!61;UBERON:0003082!9.91e-09!61;UBERON:0002385!1.37e-08!63;UBERON:0001015!1.37e-08!63;UBERON:0000383!1.37e-08!63;UBERON:0002020!1.79e-08!34;UBERON:0003528!1.79e-08!34;UBERON:0000062!1.86e-08!511;UBERON:0002100!3.16e-08!216;UBERON:0001009!5.83e-08!113;UBERON:0001893!5.85e-08!34;UBERON:0004535!7.79e-08!110;UBERON:0002791!8.54e-08!33;UBERON:0003080!8.65e-08!42;UBERON:0000064!1.12e-07!219;UBERON:0001869!1.52e-07!32;UBERON:0002780!1.76e-07!41;UBERON:0001890!1.76e-07!41;UBERON:0006240!1.76e-07!41;UBERON:0003104!6.13e-07!238;UBERON:0009142!6.13e-07!238
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}}
}}

Revision as of 19:07, 8 August 2012


Full id: C3386_gastric_Trabecular_Keratocytes_Neural_rhabdomyosarcoma_embryonic_Fibroblast



Phase1 CAGE Peaks

Hg19::chr13:80915235..80915251,-p3@SPRY2
Hg19::chr13:80915252..80915274,-p1@SPRY2
Hg19::chr13:80915289..80915300,-p4@SPRY2


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>

Uber Anatomy
Ontology termp-valuen
cell layer1.63e-24312
epithelium2.31e-24309
organism subdivision1.49e-22365
tube3.03e-21194
anatomical conduit3.49e-21241
multi-tissue structure7.72e-21347
anatomical cluster4.56e-20286
multi-cellular organism4.54e-19659
anatomical system3.51e-18625
anatomical group8.41e-18626
ectoderm-derived structure3.41e-17169
embryo8.80e-17612
ectoderm1.45e-15173
presumptive ectoderm1.45e-15173
neural plate1.53e-1586
presumptive neural plate1.53e-1586
head8.98e-15123
embryonic structure1.12e-14605
developing anatomical structure1.12e-14605
germ layer1.81e-14604
embryonic tissue1.81e-14604
presumptive structure1.81e-14604
epiblast (generic)1.81e-14604
somite2.15e-1483
paraxial mesoderm2.15e-1483
presomitic mesoderm2.15e-1483
presumptive segmental plate2.15e-1483
trunk paraxial mesoderm2.15e-1483
presumptive paraxial mesoderm2.15e-1483
neurectoderm2.42e-1390
anterior region of body3.64e-13129
craniocervical region3.64e-13129
regional part of nervous system5.33e-1394
nervous system5.33e-1394
vasculature5.61e-1379
vascular system5.61e-1379
trunk mesenchyme9.45e-13143
epithelial tube2.23e-12118
neural tube3.01e-1257
neural rod3.01e-1257
future spinal cord3.01e-1257
neural keel3.01e-1257
artery4.79e-1242
arterial blood vessel4.79e-1242
arterial system4.79e-1242
central nervous system6.22e-1282
dermomyotome1.15e-1170
vessel1.80e-1169
blood vessel7.57e-1160
epithelial tube open at both ends7.57e-1160
blood vasculature7.57e-1160
vascular cord7.57e-1160
pre-chordal neural plate1.52e-1061
regional part of brain2.71e-1059
splanchnic layer of lateral plate mesoderm2.97e-1084
systemic artery7.64e-1033
systemic arterial system7.64e-1033
multilaminar epithelium2.69e-0982
brain2.89e-0969
future brain2.89e-0969
skeletal muscle tissue9.91e-0961
striated muscle tissue9.91e-0961
myotome9.91e-0961
muscle tissue1.37e-0863
musculature1.37e-0863
musculature of body1.37e-0863
gray matter1.79e-0834
brain grey matter1.79e-0834
organ1.86e-08511
trunk3.16e-08216
circulatory system5.83e-08113
telencephalon5.85e-0834
cardiovascular system7.79e-08110
regional part of telencephalon8.54e-0833
anterior neural tube8.65e-0842
organ part1.12e-07219
cerebral hemisphere1.52e-0732
regional part of forebrain1.76e-0741
forebrain1.76e-0741
future forebrain1.76e-0741
mesenchyme6.13e-07238
entire embryonic mesenchyme6.13e-07238


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)

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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.

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