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Coexpression cluster:C4179: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.02e-45!115;UBERON:0005743!3.15e-42!86;UBERON:0000073!2.44e-41!94;UBERON:0001016!2.44e-41!94;UBERON:0001017!3.15e-40!82;UBERON:0001049!8.57e-40!57;UBERON:0005068!8.57e-40!57;UBERON:0006241!8.57e-40!57;UBERON:0007135!8.57e-40!57;UBERON:0002346!1.58e-36!90;UBERON:0003075!2.28e-36!86;UBERON:0007284!2.28e-36!86;UBERON:0000955!5.30e-34!69;UBERON:0006238!5.30e-34!69;UBERON:0002616!3.59e-33!59;UBERON:0003080!2.95e-31!42;UBERON:0002780!8.37e-31!41;UBERON:0001890!8.37e-31!41;UBERON:0006240!8.37e-31!41;UBERON:0000924!2.22e-27!173;UBERON:0006601!2.22e-27!173;UBERON:0004121!7.99e-27!169;UBERON:0000033!1.05e-25!123;UBERON:0002020!1.25e-25!34;UBERON:0003528!1.25e-25!34;UBERON:0003056!1.49e-25!61;UBERON:0001893!1.69e-25!34;UBERON:0000153!1.88e-25!129;UBERON:0007811!1.88e-25!129;UBERON:0002791!8.98e-25!33;UBERON:0001869!4.28e-24!32;UBERON:0000956!1.55e-18!25;UBERON:0000203!1.55e-18!25;UBERON:0002619!2.78e-18!22;UBERON:0001950!7.96e-17!20;UBERON:0000025!6.33e-15!194;UBERON:0000477!3.64e-14!286;UBERON:0004111!4.38e-14!241;UBERON:0000475!8.03e-13!365;UBERON:0000064!4.83e-12!219;UBERON:0000481!1.25e-11!347;UBERON:0000468!9.39e-11!659;UBERON:0000483!6.07e-10!309;UBERON:0000922!8.54e-10!612;UBERON:0003076!1.42e-09!15;UBERON:0003057!1.42e-09!15;UBERON:0000062!1.71e-09!511;UBERON:0000119!1.80e-09!312;UBERON:0002420!1.13e-08!9;UBERON:0007245!1.13e-08!9;UBERON:0010009!1.13e-08!9;UBERON:0010011!1.13e-08!9;UBERON:0000454!1.13e-08!9;UBERON:0002308!1.47e-08!9;UBERON:0000125!1.47e-08!9;UBERON:0002050!3.24e-08!605;UBERON:0005423!3.24e-08!605;UBERON:0000923!5.94e-08!604;UBERON:0005291!5.94e-08!604;UBERON:0006598!5.94e-08!604;UBERON:0002532!5.94e-08!604;UBERON:0004732!7.25e-08!13;UBERON:0004733!1.87e-07!12;UBERON:0002028!1.87e-07!12;UBERON:0007277!1.87e-07!12;UBERON:0001871!2.05e-07!7;UBERON:0000467!3.39e-07!625;UBERON:0002298!4.17e-07!8;UBERON:0000480!4.41e-07!626;UBERON:0009663!4.81e-07!7
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}}
}}

Revision as of 19:48, 8 August 2012


Full id: C4179_pineal_cerebellum_adrenal_gastric_kidney_seminal_duodenum



Phase1 CAGE Peaks

Hg19::chr2:213403880..213403914,-p1@ERBB4
Hg19::chr2:213403969..213403990,-p4@ERBB4
Hg19::chr2:213403991..213404019,-p5@ERBB4


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 organism3.02e-45115
regional part of nervous system2.44e-4194
nervous system2.44e-4194
central nervous system3.15e-4082
neural tube8.57e-4057
neural rod8.57e-4057
future spinal cord8.57e-4057
neural keel8.57e-4057
neurectoderm1.58e-3690
neural plate2.28e-3686
presumptive neural plate2.28e-3686
brain5.30e-3469
future brain5.30e-3469
regional part of brain3.59e-3359
anterior neural tube2.95e-3142
regional part of forebrain8.37e-3141
forebrain8.37e-3141
future forebrain8.37e-3141
ectoderm2.22e-27173
presumptive ectoderm2.22e-27173
ectoderm-derived structure7.99e-27169
head1.05e-25123
gray matter1.25e-2534
brain grey matter1.25e-2534
pre-chordal neural plate1.49e-2561
telencephalon1.69e-2534
anterior region of body1.88e-25129
craniocervical region1.88e-25129
regional part of telencephalon8.98e-2533
cerebral hemisphere4.28e-2432
cerebral cortex1.55e-1825
pallium1.55e-1825
regional part of cerebral cortex2.78e-1822
neocortex7.96e-1720
tube6.33e-15194
anatomical cluster3.64e-14286
anatomical conduit4.38e-14241
organism subdivision8.03e-13365
organ part4.83e-12219
multi-tissue structure1.25e-11347
multi-cellular organism9.39e-11659
epithelium6.07e-10309
embryo8.54e-10612
posterior neural tube1.42e-0915
chordal neural plate1.42e-0915
organ1.71e-09511
cell layer1.80e-09312
basal ganglion1.13e-089
nuclear complex of neuraxis1.13e-089
aggregate regional part of brain1.13e-089
collection of basal ganglia1.13e-089
cerebral subcortex1.13e-089
nucleus of brain1.47e-089
neural nucleus1.47e-089
embryonic structure3.24e-08605
developing anatomical structure3.24e-08605
germ layer5.94e-08604
embryonic tissue5.94e-08604
presumptive structure5.94e-08604
epiblast (generic)5.94e-08604
segmental subdivision of nervous system7.25e-0813
segmental subdivision of hindbrain1.87e-0712
hindbrain1.87e-0712
presumptive hindbrain1.87e-0712
temporal lobe2.05e-077
anatomical system3.39e-07625
brainstem4.17e-078
anatomical group4.41e-07626
telencephalic nucleus4.81e-077


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.