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Coexpression cluster:C2951: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.55e-34!115;UBERON:0001049!2.07e-32!57;UBERON:0005068!2.07e-32!57;UBERON:0006241!2.07e-32!57;UBERON:0007135!2.07e-32!57;UBERON:0001017!4.58e-32!82;UBERON:0005743!5.20e-32!86;UBERON:0000073!2.02e-30!94;UBERON:0001016!2.02e-30!94;UBERON:0000955!3.11e-28!69;UBERON:0006238!3.11e-28!69;UBERON:0002616!4.86e-28!59;UBERON:0000924!5.07e-28!173;UBERON:0006601!5.07e-28!173;UBERON:0002346!7.88e-28!90;UBERON:0003075!1.78e-27!86;UBERON:0007284!1.78e-27!86;UBERON:0004121!2.01e-27!169;UBERON:0003080!1.49e-24!42;UBERON:0002780!2.91e-24!41;UBERON:0001890!2.91e-24!41;UBERON:0006240!2.91e-24!41;UBERON:0000153!4.51e-22!129;UBERON:0007811!4.51e-22!129;UBERON:0000033!2.04e-21!123;UBERON:0002020!5.69e-21!34;UBERON:0003528!5.69e-21!34;UBERON:0001893!6.76e-21!34;UBERON:0003056!1.20e-20!61;UBERON:0002791!2.49e-20!33;UBERON:0001869!1.15e-19!32;UBERON:0000956!1.84e-15!25;UBERON:0000203!1.84e-15!25;UBERON:0002619!5.45e-14!22;UBERON:0001950!8.69e-13!20;UBERON:0000064!1.61e-12!219;UBERON:0000475!2.73e-12!365;UBERON:0000062!5.02e-11!511;UBERON:0000468!1.13e-09!659;UBERON:0000481!4.09e-09!347;UBERON:0003076!6.33e-09!15;UBERON:0003057!6.33e-09!15;UBERON:0000025!6.85e-09!194;UBERON:0000477!1.80e-08!286;UBERON:0005631!2.66e-08!14;UBERON:0000158!2.66e-08!14;UBERON:0000483!3.52e-08!309;UBERON:0000119!3.86e-08!312;UBERON:0004111!4.16e-08!241;UBERON:0004732!1.12e-07!13;UBERON:0000480!2.56e-07!626;UBERON:0000467!2.97e-07!625;UBERON:0004733!3.20e-07!12;UBERON:0002028!3.20e-07!12;UBERON:0007277!3.20e-07!12;UBERON:0002308!5.56e-07!9;UBERON:0000125!5.56e-07!9;UBERON:0002420!7.06e-07!9;UBERON:0007245!7.06e-07!9;UBERON:0010009!7.06e-07!9;UBERON:0010011!7.06e-07!9;UBERON:0000454!7.06e-07!9
|ontology_enrichment_uberon=UBERON:0007023!8.55e-34!115;UBERON:0001049!2.07e-32!57;UBERON:0005068!2.07e-32!57;UBERON:0006241!2.07e-32!57;UBERON:0007135!2.07e-32!57;UBERON:0001017!4.58e-32!82;UBERON:0005743!5.20e-32!86;UBERON:0000073!2.02e-30!94;UBERON:0001016!2.02e-30!94;UBERON:0000955!3.11e-28!69;UBERON:0006238!3.11e-28!69;UBERON:0002616!4.86e-28!59;UBERON:0000924!5.07e-28!173;UBERON:0006601!5.07e-28!173;UBERON:0002346!7.88e-28!90;UBERON:0003075!1.78e-27!86;UBERON:0007284!1.78e-27!86;UBERON:0004121!2.01e-27!169;UBERON:0003080!1.49e-24!42;UBERON:0002780!2.91e-24!41;UBERON:0001890!2.91e-24!41;UBERON:0006240!2.91e-24!41;UBERON:0000153!4.51e-22!129;UBERON:0007811!4.51e-22!129;UBERON:0000033!2.04e-21!123;UBERON:0002020!5.69e-21!34;UBERON:0003528!5.69e-21!34;UBERON:0001893!6.76e-21!34;UBERON:0003056!1.20e-20!61;UBERON:0002791!2.49e-20!33;UBERON:0001869!1.15e-19!32;UBERON:0000956!1.84e-15!25;UBERON:0000203!1.84e-15!25;UBERON:0002619!5.45e-14!22;UBERON:0001950!8.69e-13!20;UBERON:0000064!1.61e-12!219;UBERON:0000475!2.73e-12!365;UBERON:0000062!5.02e-11!511;UBERON:0000468!1.13e-09!659;UBERON:0000481!4.09e-09!347;UBERON:0003076!6.33e-09!15;UBERON:0003057!6.33e-09!15;UBERON:0000025!6.85e-09!194;UBERON:0000477!1.80e-08!286;UBERON:0005631!2.66e-08!14;UBERON:0000158!2.66e-08!14;UBERON:0000483!3.52e-08!309;UBERON:0000119!3.86e-08!312;UBERON:0004111!4.16e-08!241;UBERON:0004732!1.12e-07!13;UBERON:0000480!2.56e-07!626;UBERON:0000467!2.97e-07!625;UBERON:0004733!3.20e-07!12;UBERON:0002028!3.20e-07!12;UBERON:0007277!3.20e-07!12;UBERON:0002308!5.56e-07!9;UBERON:0000125!5.56e-07!9;UBERON:0002420!7.06e-07!9;UBERON:0007245!7.06e-07!9;UBERON:0010009!7.06e-07!9;UBERON:0010011!7.06e-07!9;UBERON:0000454!7.06e-07!9
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}}
}}

Revision as of 13:44, 5 September 2012


Full id: C2951_epididymis_ductus_embryonic_seminal_Amniotic_locus_diaphragm



Phase1 CAGE Peaks

Hg19::chrX:112083964..112083975,-p6@AMOT
Hg19::chrX:112084001..112084012,-p4@AMOT
Hg19::chrX:112084017..112084031,-p3@AMOT
Hg19::chrX:112084045..112084071,-p1@AMOT


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 organism8.55e-34115
neural tube2.07e-3257
neural rod2.07e-3257
future spinal cord2.07e-3257
neural keel2.07e-3257
central nervous system4.58e-3282
regional part of nervous system2.02e-3094
nervous system2.02e-3094
brain3.11e-2869
future brain3.11e-2869
regional part of brain4.86e-2859
ectoderm5.07e-28173
presumptive ectoderm5.07e-28173
neurectoderm7.88e-2890
neural plate1.78e-2786
presumptive neural plate1.78e-2786
ectoderm-derived structure2.01e-27169
anterior neural tube1.49e-2442
regional part of forebrain2.91e-2441
forebrain2.91e-2441
future forebrain2.91e-2441
anterior region of body4.51e-22129
craniocervical region4.51e-22129
head2.04e-21123
gray matter5.69e-2134
brain grey matter5.69e-2134
telencephalon6.76e-2134
pre-chordal neural plate1.20e-2061
regional part of telencephalon2.49e-2033
cerebral hemisphere1.15e-1932
cerebral cortex1.84e-1525
pallium1.84e-1525
regional part of cerebral cortex5.45e-1422
neocortex8.69e-1320
organ part1.61e-12219
organism subdivision2.73e-12365
organ5.02e-11511
multi-cellular organism1.13e-09659
multi-tissue structure4.09e-09347
posterior neural tube6.33e-0915
chordal neural plate6.33e-0915
tube6.85e-09194
anatomical cluster1.80e-08286
extraembryonic membrane2.66e-0814
membranous layer2.66e-0814
epithelium3.52e-08309
cell layer3.86e-08312
anatomical conduit4.16e-08241
segmental subdivision of nervous system1.12e-0713
anatomical group2.56e-07626
anatomical system2.97e-07625
segmental subdivision of hindbrain3.20e-0712
hindbrain3.20e-0712
presumptive hindbrain3.20e-0712
nucleus of brain5.56e-079
neural nucleus5.56e-079
basal ganglion7.06e-079
nuclear complex of neuraxis7.06e-079
aggregate regional part of brain7.06e-079
collection of basal ganglia7.06e-079
cerebral subcortex7.06e-079


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
CTBP2#1488462.71700033932816.45042639894877e-083.97214671391398e-06
ZNF263#1012748.221841637010680.0002187871180958320.00250272812999021



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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