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Coexpression cluster:C2825: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.02e-39!115;UBERON:0001049!7.30e-18!57;UBERON:0005068!7.30e-18!57;UBERON:0006241!7.30e-18!57;UBERON:0007135!7.30e-18!57;UBERON:0002616!1.10e-16!59;UBERON:0000477!1.41e-16!286;UBERON:0002780!1.84e-16!41;UBERON:0001890!1.84e-16!41;UBERON:0006240!1.84e-16!41;UBERON:0003075!2.03e-16!86;UBERON:0007284!2.03e-16!86;UBERON:0003080!9.22e-16!42;UBERON:0005743!1.15e-15!86;UBERON:0001017!1.21e-15!82;UBERON:0002346!1.93e-15!90;UBERON:0001893!1.03e-14!34;UBERON:0000955!1.92e-14!69;UBERON:0006238!1.92e-14!69;UBERON:0002020!2.36e-14!34;UBERON:0003528!2.36e-14!34;UBERON:0001869!2.67e-14!32;UBERON:0002791!4.54e-14!33;UBERON:0001950!1.73e-13!20;UBERON:0000481!7.09e-13!347;UBERON:0002619!7.78e-13!22;UBERON:0000073!2.12e-12!94;UBERON:0001016!2.12e-12!94;UBERON:0000064!3.58e-12!219;UBERON:0000956!2.13e-11!25;UBERON:0000203!2.13e-11!25;UBERON:0003056!2.70e-11!61;UBERON:0000062!6.49e-11!511;UBERON:0004111!9.92e-11!241;UBERON:0000153!3.91e-10!129;UBERON:0007811!3.91e-10!129;UBERON:0001737!9.52e-10!9;UBERON:0000468!1.12e-09!659;UBERON:0000467!1.25e-09!625;UBERON:0000480!1.63e-09!626;UBERON:0000033!1.80e-09!123;UBERON:0004121!1.85e-09!169;UBERON:0004921!2.58e-09!129;UBERON:0004185!2.58e-09!129;UBERON:0000924!4.28e-09!173;UBERON:0006601!4.28e-09!173;UBERON:0001007!6.69e-09!155;UBERON:0001555!6.69e-09!155;UBERON:0007026!6.69e-09!155;UBERON:0000922!9.44e-09!612;UBERON:0002050!4.18e-08!605;UBERON:0005423!4.18e-08!605;UBERON:0004119!4.25e-08!169;UBERON:0000925!4.25e-08!169;UBERON:0006595!4.25e-08!169;UBERON:0000923!7.30e-08!604;UBERON:0005291!7.30e-08!604;UBERON:0006598!7.30e-08!604;UBERON:0002532!7.30e-08!604;UBERON:0001557!9.25e-08!19;UBERON:0000025!1.46e-07!194;UBERON:0000483!4.76e-07!309;UBERON:0000119!6.20e-07!312;UBERON:0000077!6.63e-07!130
|ontology_enrichment_uberon=UBERON:0007023!2.02e-39!115;UBERON:0001049!7.30e-18!57;UBERON:0005068!7.30e-18!57;UBERON:0006241!7.30e-18!57;UBERON:0007135!7.30e-18!57;UBERON:0002616!1.10e-16!59;UBERON:0000477!1.41e-16!286;UBERON:0002780!1.84e-16!41;UBERON:0001890!1.84e-16!41;UBERON:0006240!1.84e-16!41;UBERON:0003075!2.03e-16!86;UBERON:0007284!2.03e-16!86;UBERON:0003080!9.22e-16!42;UBERON:0005743!1.15e-15!86;UBERON:0001017!1.21e-15!82;UBERON:0002346!1.93e-15!90;UBERON:0001893!1.03e-14!34;UBERON:0000955!1.92e-14!69;UBERON:0006238!1.92e-14!69;UBERON:0002020!2.36e-14!34;UBERON:0003528!2.36e-14!34;UBERON:0001869!2.67e-14!32;UBERON:0002791!4.54e-14!33;UBERON:0001950!1.73e-13!20;UBERON:0000481!7.09e-13!347;UBERON:0002619!7.78e-13!22;UBERON:0000073!2.12e-12!94;UBERON:0001016!2.12e-12!94;UBERON:0000064!3.58e-12!219;UBERON:0000956!2.13e-11!25;UBERON:0000203!2.13e-11!25;UBERON:0003056!2.70e-11!61;UBERON:0000062!6.49e-11!511;UBERON:0004111!9.92e-11!241;UBERON:0000153!3.91e-10!129;UBERON:0007811!3.91e-10!129;UBERON:0001737!9.52e-10!9;UBERON:0000468!1.12e-09!659;UBERON:0000467!1.25e-09!625;UBERON:0000480!1.63e-09!626;UBERON:0000033!1.80e-09!123;UBERON:0004121!1.85e-09!169;UBERON:0004921!2.58e-09!129;UBERON:0004185!2.58e-09!129;UBERON:0000924!4.28e-09!173;UBERON:0006601!4.28e-09!173;UBERON:0001007!6.69e-09!155;UBERON:0001555!6.69e-09!155;UBERON:0007026!6.69e-09!155;UBERON:0000922!9.44e-09!612;UBERON:0002050!4.18e-08!605;UBERON:0005423!4.18e-08!605;UBERON:0004119!4.25e-08!169;UBERON:0000925!4.25e-08!169;UBERON:0006595!4.25e-08!169;UBERON:0000923!7.30e-08!604;UBERON:0005291!7.30e-08!604;UBERON:0006598!7.30e-08!604;UBERON:0002532!7.30e-08!604;UBERON:0001557!9.25e-08!19;UBERON:0000025!1.46e-07!194;UBERON:0000483!4.76e-07!309;UBERON:0000119!6.20e-07!312;UBERON:0000077!6.63e-07!130
|tf_chipseq_enrich=GATA3#2625;4:27.236516357206:1.81561517799785e-06:6.78672274784957e-05!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000444079077739603!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024490764305245!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114765301871352
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}}
}}

Revision as of 13:22, 5 September 2012


Full id: C2825_cervical_gall_bile_rectal_epitheloid_large_umbilical



Phase1 CAGE Peaks

Hg19::chr5:58571724..58571727,-p8@uc003jsd.1
Hg19::chr5:58571770..58571781,-p7@uc003jsd.1
Hg19::chr5:58571807..58571821,-p24@PDE4D
Hg19::chr5:58571829..58571862,-p9@PDE4D


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

GO IDGO nameFDR corrected p-value
GO:00041153',5'-cyclic-AMP phosphodiesterase activity0.00638761332862357
GO:0005626insoluble fraction0.00912516189803367
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0107220652301896
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0107220652301896
GO:0005813centrosome0.0191628399858707
GO:0008081phosphoric diester hydrolase activity0.0191628399858707
GO:0005815microtubule organizing center0.0191628399858707
GO:0005625soluble fraction0.0266910985517485



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 organism2.02e-39115
neural tube7.30e-1857
neural rod7.30e-1857
future spinal cord7.30e-1857
neural keel7.30e-1857
regional part of brain1.10e-1659
anatomical cluster1.41e-16286
regional part of forebrain1.84e-1641
forebrain1.84e-1641
future forebrain1.84e-1641
neural plate2.03e-1686
presumptive neural plate2.03e-1686
anterior neural tube9.22e-1642
central nervous system1.21e-1582
neurectoderm1.93e-1590
telencephalon1.03e-1434
brain1.92e-1469
future brain1.92e-1469
gray matter2.36e-1434
brain grey matter2.36e-1434
cerebral hemisphere2.67e-1432
regional part of telencephalon4.54e-1433
neocortex1.73e-1320
multi-tissue structure7.09e-13347
regional part of cerebral cortex7.78e-1322
regional part of nervous system2.12e-1294
nervous system2.12e-1294
organ part3.58e-12219
cerebral cortex2.13e-1125
pallium2.13e-1125
pre-chordal neural plate2.70e-1161
organ6.49e-11511
anatomical conduit9.92e-11241
anterior region of body3.91e-10129
craniocervical region3.91e-10129
larynx9.52e-109
multi-cellular organism1.12e-09659
anatomical system1.25e-09625
anatomical group1.63e-09626
head1.80e-09123
ectoderm-derived structure1.85e-09169
subdivision of digestive tract2.58e-09129
endodermal part of digestive tract2.58e-09129
ectoderm4.28e-09173
presumptive ectoderm4.28e-09173
digestive system6.69e-09155
digestive tract6.69e-09155
primitive gut6.69e-09155
embryo9.44e-09612
embryonic structure4.18e-08605
developing anatomical structure4.18e-08605
endoderm-derived structure4.25e-08169
endoderm4.25e-08169
presumptive endoderm4.25e-08169
germ layer7.30e-08604
embryonic tissue7.30e-08604
presumptive structure7.30e-08604
epiblast (generic)7.30e-08604
upper respiratory tract9.25e-0819
tube1.46e-07194
epithelium4.76e-07309
cell layer6.20e-07312
mixed endoderm/mesoderm-derived structure6.63e-07130


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
GATA3#2625427.2365163572061.81561517799785e-066.78672274784957e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000444079077739603
TBP#690843.706770687096390.005296377814784350.024490764305245
TFAP2C#7022410.80922860986027.32289634782688e-050.00114765301871352



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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