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Coexpression cluster:C355: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.53e-47!115;UBERON:0005743!1.34e-31!86;UBERON:0001017!2.37e-31!82;UBERON:0001049!1.04e-30!57;UBERON:0005068!1.04e-30!57;UBERON:0006241!1.04e-30!57;UBERON:0007135!1.04e-30!57;UBERON:0003075!3.08e-29!86;UBERON:0007284!3.08e-29!86;UBERON:0000073!1.86e-27!94;UBERON:0001016!1.86e-27!94;UBERON:0002616!1.71e-26!59;UBERON:0000955!3.90e-26!69;UBERON:0006238!3.90e-26!69;UBERON:0002346!4.64e-26!90;UBERON:0003080!1.01e-22!42;UBERON:0002780!1.80e-22!41;UBERON:0001890!1.80e-22!41;UBERON:0006240!1.80e-22!41;UBERON:0000477!4.18e-22!286;UBERON:0000033!1.87e-21!123;UBERON:0000153!2.55e-21!129;UBERON:0007811!2.55e-21!129;UBERON:0003056!4.50e-21!61;UBERON:0002020!1.14e-19!34;UBERON:0003528!1.14e-19!34;UBERON:0001893!2.12e-19!34;UBERON:0002791!6.31e-19!33;UBERON:0001869!2.55e-18!32;UBERON:0000468!4.89e-18!659;UBERON:0004121!8.79e-18!169;UBERON:0004111!2.21e-17!241;UBERON:0000924!2.91e-16!173;UBERON:0006601!2.91e-16!173;UBERON:0000025!8.74e-15!194;UBERON:0000956!1.36e-14!25;UBERON:0000203!1.36e-14!25;UBERON:0000467!8.59e-14!625;UBERON:0000480!8.95e-14!626;UBERON:0000064!2.45e-13!219;UBERON:0002619!2.81e-13!22;UBERON:0000481!4.05e-13!347;UBERON:0000475!1.38e-12!365;UBERON:0001950!5.29e-12!20;UBERON:0000922!5.50e-12!612;UBERON:0002050!1.50e-10!605;UBERON:0005423!1.50e-10!605;UBERON:0000062!1.66e-10!511;UBERON:0000923!2.21e-10!604;UBERON:0005291!2.21e-10!604;UBERON:0006598!2.21e-10!604;UBERON:0002532!2.21e-10!604;UBERON:0000483!1.37e-09!309;UBERON:0000119!2.00e-09!312;UBERON:0003076!4.50e-09!15;UBERON:0003057!4.50e-09!15;UBERON:0004732!1.51e-07!13;UBERON:0004733!3.47e-07!12;UBERON:0002028!3.47e-07!12;UBERON:0007277!3.47e-07!12
|ontology_enrichment_uberon=UBERON:0007023!3.53e-47!115;UBERON:0005743!1.34e-31!86;UBERON:0001017!2.37e-31!82;UBERON:0001049!1.04e-30!57;UBERON:0005068!1.04e-30!57;UBERON:0006241!1.04e-30!57;UBERON:0007135!1.04e-30!57;UBERON:0003075!3.08e-29!86;UBERON:0007284!3.08e-29!86;UBERON:0000073!1.86e-27!94;UBERON:0001016!1.86e-27!94;UBERON:0002616!1.71e-26!59;UBERON:0000955!3.90e-26!69;UBERON:0006238!3.90e-26!69;UBERON:0002346!4.64e-26!90;UBERON:0003080!1.01e-22!42;UBERON:0002780!1.80e-22!41;UBERON:0001890!1.80e-22!41;UBERON:0006240!1.80e-22!41;UBERON:0000477!4.18e-22!286;UBERON:0000033!1.87e-21!123;UBERON:0000153!2.55e-21!129;UBERON:0007811!2.55e-21!129;UBERON:0003056!4.50e-21!61;UBERON:0002020!1.14e-19!34;UBERON:0003528!1.14e-19!34;UBERON:0001893!2.12e-19!34;UBERON:0002791!6.31e-19!33;UBERON:0001869!2.55e-18!32;UBERON:0000468!4.89e-18!659;UBERON:0004121!8.79e-18!169;UBERON:0004111!2.21e-17!241;UBERON:0000924!2.91e-16!173;UBERON:0006601!2.91e-16!173;UBERON:0000025!8.74e-15!194;UBERON:0000956!1.36e-14!25;UBERON:0000203!1.36e-14!25;UBERON:0000467!8.59e-14!625;UBERON:0000480!8.95e-14!626;UBERON:0000064!2.45e-13!219;UBERON:0002619!2.81e-13!22;UBERON:0000481!4.05e-13!347;UBERON:0000475!1.38e-12!365;UBERON:0001950!5.29e-12!20;UBERON:0000922!5.50e-12!612;UBERON:0002050!1.50e-10!605;UBERON:0005423!1.50e-10!605;UBERON:0000062!1.66e-10!511;UBERON:0000923!2.21e-10!604;UBERON:0005291!2.21e-10!604;UBERON:0006598!2.21e-10!604;UBERON:0002532!2.21e-10!604;UBERON:0000483!1.37e-09!309;UBERON:0000119!2.00e-09!312;UBERON:0003076!4.50e-09!15;UBERON:0003057!4.50e-09!15;UBERON:0004732!1.51e-07!13;UBERON:0004733!3.47e-07!12;UBERON:0002028!3.47e-07!12;UBERON:0007277!3.47e-07!12
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}}
}}

Revision as of 19:16, 8 August 2012


Full id: C355_Chondrocyte_Hepatocyte_spinal_medulla_cerebral_seminal_hippocampus



Phase1 CAGE Peaks

Hg19::chr8:27455536..27455576,-p@chr8:27455536..27455576
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Hg19::chr8:27455583..27455667,-p@chr8:27455583..27455667
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Hg19::chr8:27455692..27455710,-p@chr8:27455692..27455710
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Hg19::chr8:27455711..27455732,-p@chr8:27455711..27455732
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Hg19::chr8:27456058..27456137,-p@chr8:27456058..27456137
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Hg19::chr8:27456141..27456161,-p@chr8:27456141..27456161
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Hg19::chr8:27457336..27457372,-p@chr8:27457336..27457372
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Hg19::chr8:27457396..27457456,-p@chr8:27457396..27457456
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Hg19::chr8:27457470..27457493,-p@chr8:27457470..27457493
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Hg19::chr8:27457494..27457531,-p@chr8:27457494..27457531
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Hg19::chr8:27461872..27461920,-p@chr8:27461872..27461920
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Hg19::chr8:27462566..27462587,-p24@CLU
Hg19::chr8:27462617..27462687,-p9@CLU
Hg19::chr8:27462692..27462746,-p14@CLU
Hg19::chr8:27462747..27462758,-p31@CLU
Hg19::chr8:27462773..27462781,-p28@CLU
Hg19::chr8:27462787..27462819,-p20@CLU
Hg19::chr8:27462822..27462853,-p10@CLU
Hg19::chr8:27463908..27463929,-p18@CLU
Hg19::chr8:27463932..27463992,-p4@CLU
Hg19::chr8:27463995..27464033,-p15@CLU
Hg19::chr8:27464034..27464046,-p25@CLU
Hg19::chr8:27466494..27466506,-p17@CLU
Hg19::chr8:27466535..27466550,-p5@CLU
Hg19::chr8:27466559..27466562,-p44@CLU
Hg19::chr8:27466559..27466566,+p@chr8:27466559..27466566
+
Hg19::chr8:27466577..27466595,-p8@CLU
Hg19::chr8:27466597..27466608,-p23@CLU
Hg19::chr8:27468013..27468046,-p6@CLU
Hg19::chr8:27468052..27468067,-p13@CLU
Hg19::chr8:27468075..27468130,-p7@CLU
Hg19::chr8:27472209..27472225,-p1@CLU


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
adult organism3.53e-47115
central nervous system2.37e-3182
neural tube1.04e-3057
neural rod1.04e-3057
future spinal cord1.04e-3057
neural keel1.04e-3057
neural plate3.08e-2986
presumptive neural plate3.08e-2986
regional part of nervous system1.86e-2794
nervous system1.86e-2794
regional part of brain1.71e-2659
brain3.90e-2669
future brain3.90e-2669
neurectoderm4.64e-2690
anterior neural tube1.01e-2242
regional part of forebrain1.80e-2241
forebrain1.80e-2241
future forebrain1.80e-2241
anatomical cluster4.18e-22286
head1.87e-21123
anterior region of body2.55e-21129
craniocervical region2.55e-21129
pre-chordal neural plate4.50e-2161
gray matter1.14e-1934
brain grey matter1.14e-1934
telencephalon2.12e-1934
regional part of telencephalon6.31e-1933
cerebral hemisphere2.55e-1832
multi-cellular organism4.89e-18659
ectoderm-derived structure8.79e-18169
anatomical conduit2.21e-17241
ectoderm2.91e-16173
presumptive ectoderm2.91e-16173
tube8.74e-15194
cerebral cortex1.36e-1425
pallium1.36e-1425
anatomical system8.59e-14625
anatomical group8.95e-14626
organ part2.45e-13219
regional part of cerebral cortex2.81e-1322
multi-tissue structure4.05e-13347
organism subdivision1.38e-12365
neocortex5.29e-1220
embryo5.50e-12612
embryonic structure1.50e-10605
developing anatomical structure1.50e-10605
organ1.66e-10511
germ layer2.21e-10604
embryonic tissue2.21e-10604
presumptive structure2.21e-10604
epiblast (generic)2.21e-10604
epithelium1.37e-09309
cell layer2.00e-09312
posterior neural tube4.50e-0915
chordal neural plate4.50e-0915
segmental subdivision of nervous system1.51e-0713
segmental subdivision of hindbrain3.47e-0712
hindbrain3.47e-0712
presumptive hindbrain3.47e-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.

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