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Coexpression cluster:C2291: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!6.91e-48!94;UBERON:0001016!6.91e-48!94;UBERON:0005743!1.19e-47!86;UBERON:0001017!5.34e-47!82;UBERON:0001049!1.13e-45!57;UBERON:0005068!1.13e-45!57;UBERON:0006241!1.13e-45!57;UBERON:0007135!1.13e-45!57;UBERON:0003075!2.06e-42!86;UBERON:0007284!2.06e-42!86;UBERON:0002346!1.73e-41!90;UBERON:0007023!6.82e-39!115;UBERON:0002616!3.59e-38!59;UBERON:0000955!5.68e-36!69;UBERON:0006238!5.68e-36!69;UBERON:0003080!7.73e-35!42;UBERON:0004121!3.75e-34!169;UBERON:0002780!4.61e-34!41;UBERON:0001890!4.61e-34!41;UBERON:0006240!4.61e-34!41;UBERON:0000924!4.75e-34!173;UBERON:0006601!4.75e-34!173;UBERON:0003056!8.44e-32!61;UBERON:0000033!1.22e-29!123;UBERON:0002020!3.51e-29!34;UBERON:0003528!3.51e-29!34;UBERON:0001893!6.75e-29!34;UBERON:0000153!7.05e-29!129;UBERON:0007811!7.05e-29!129;UBERON:0002791!4.44e-28!33;UBERON:0001869!2.66e-27!32;UBERON:0000956!1.78e-21!25;UBERON:0000203!1.78e-21!25;UBERON:0002619!5.96e-20!22;UBERON:0001950!3.86e-18!20;UBERON:0000481!1.89e-14!347;UBERON:0000475!2.68e-14!365;UBERON:0000483!1.02e-13!309;UBERON:0000119!1.44e-13!312;UBERON:0000922!1.90e-13!612;UBERON:0000025!7.67e-12!194;UBERON:0003076!1.13e-11!15;UBERON:0003057!1.13e-11!15;UBERON:0004111!1.27e-11!241;UBERON:0002050!5.89e-11!605;UBERON:0005423!5.89e-11!605;UBERON:0000923!1.30e-10!604;UBERON:0005291!1.30e-10!604;UBERON:0006598!1.30e-10!604;UBERON:0002532!1.30e-10!604;UBERON:0000468!2.03e-10!659;UBERON:0000477!2.06e-10!286;UBERON:0004732!1.17e-09!13;UBERON:0002308!4.04e-09!9;UBERON:0000125!4.04e-09!9;UBERON:0002420!4.56e-09!9;UBERON:0007245!4.56e-09!9;UBERON:0010009!4.56e-09!9;UBERON:0010011!4.56e-09!9;UBERON:0000454!4.56e-09!9;UBERON:0004733!6.33e-09!12;UBERON:0002028!6.33e-09!12;UBERON:0007277!6.33e-09!12;UBERON:0002298!3.02e-08!8;UBERON:0000467!1.57e-07!625;UBERON:0000480!1.97e-07!626;UBERON:0009663!2.90e-07!7;UBERON:0000064!4.65e-07!219;UBERON:0000200!5.41e-07!6;UBERON:0000062!5.75e-07!511
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}}
}}

Revision as of 18:10, 8 August 2012


Full id: C2291_parietal_Neural_occipital_medial_spinal_locus_temporal



Phase1 CAGE Peaks

Hg19::chr14:27066880..27066891,-p12@NOVA1
Hg19::chr14:27066907..27066914,-p18@NOVA1
Hg19::chr14:27066917..27066929,-p15@NOVA1
Hg19::chr7:121651047..121651081,+p7@PTPRZ1


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:0019198transmembrane receptor protein phosphatase activity0.041376059867355
GO:0005001transmembrane receptor protein tyrosine phosphatase activity0.041376059867355



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
neuronal stem cell5.02e-088
neural cell5.64e-0825
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.91e-4894
nervous system6.91e-4894
central nervous system5.34e-4782
neural tube1.13e-4557
neural rod1.13e-4557
future spinal cord1.13e-4557
neural keel1.13e-4557
neural plate2.06e-4286
presumptive neural plate2.06e-4286
neurectoderm1.73e-4190
adult organism6.82e-39115
regional part of brain3.59e-3859
brain5.68e-3669
future brain5.68e-3669
anterior neural tube7.73e-3542
ectoderm-derived structure3.75e-34169
regional part of forebrain4.61e-3441
forebrain4.61e-3441
future forebrain4.61e-3441
ectoderm4.75e-34173
presumptive ectoderm4.75e-34173
pre-chordal neural plate8.44e-3261
head1.22e-29123
gray matter3.51e-2934
brain grey matter3.51e-2934
telencephalon6.75e-2934
anterior region of body7.05e-29129
craniocervical region7.05e-29129
regional part of telencephalon4.44e-2833
cerebral hemisphere2.66e-2732
cerebral cortex1.78e-2125
pallium1.78e-2125
regional part of cerebral cortex5.96e-2022
neocortex3.86e-1820
multi-tissue structure1.89e-14347
organism subdivision2.68e-14365
epithelium1.02e-13309
cell layer1.44e-13312
embryo1.90e-13612
tube7.67e-12194
posterior neural tube1.13e-1115
chordal neural plate1.13e-1115
anatomical conduit1.27e-11241
embryonic structure5.89e-11605
developing anatomical structure5.89e-11605
germ layer1.30e-10604
embryonic tissue1.30e-10604
presumptive structure1.30e-10604
epiblast (generic)1.30e-10604
multi-cellular organism2.03e-10659
anatomical cluster2.06e-10286
segmental subdivision of nervous system1.17e-0913
nucleus of brain4.04e-099
neural nucleus4.04e-099
basal ganglion4.56e-099
nuclear complex of neuraxis4.56e-099
aggregate regional part of brain4.56e-099
collection of basal ganglia4.56e-099
cerebral subcortex4.56e-099
segmental subdivision of hindbrain6.33e-0912
hindbrain6.33e-0912
presumptive hindbrain6.33e-0912
brainstem3.02e-088
anatomical system1.57e-07625
anatomical group1.97e-07626
telencephalic nucleus2.90e-077
organ part4.65e-07219
gyrus5.41e-076
organ5.75e-07511


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.