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Coexpression cluster:C1073: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000468!2.09e-25!656;UBERON:0000477!3.98e-22!373;UBERON:0000467!2.06e-21!624;UBERON:0000480!5.62e-21!625;UBERON:0004111!8.80e-21!240;UBERON:0001049!5.58e-20!56;UBERON:0005068!5.58e-20!56;UBERON:0006241!5.58e-20!56;UBERON:0007135!5.58e-20!56;UBERON:0000073!1.52e-18!53;UBERON:0002616!1.52e-18!53;UBERON:0000922!2.77e-18!592;UBERON:0001017!2.43e-17!81;UBERON:0002780!3.90e-17!41;UBERON:0001890!3.90e-17!41;UBERON:0003080!3.90e-17!41;UBERON:0006240!3.90e-17!41;UBERON:0004121!1.35e-16!171;UBERON:0000924!1.35e-16!171;UBERON:0006601!1.35e-16!171;UBERON:0001016!1.77e-16!89;UBERON:0003528!2.35e-16!34;UBERON:0002020!2.35e-16!34;UBERON:0002346!4.61e-16!86;UBERON:0005423!4.89e-16!581;UBERON:0002050!7.44e-16!564;UBERON:0010371!8.73e-16!104;UBERON:0003075!1.10e-15!82;UBERON:0007284!1.10e-15!82;UBERON:0001893!1.24e-15!34;UBERON:0000955!2.61e-15!68;UBERON:0006238!2.61e-15!68;UBERON:0002791!2.75e-15!32;UBERON:0007023!3.32e-15!114;UBERON:0000923!3.35e-15!560;UBERON:0010316!3.35e-15!560;UBERON:0005291!3.35e-15!560;UBERON:0006598!3.35e-15!560;UBERON:0010317!3.35e-15!560;UBERON:0002532!3.35e-15!560;UBERON:0000025!4.03e-15!192;UBERON:0001869!5.90e-15!32;UBERON:0010314!3.54e-14!132;UBERON:0000062!6.07e-14!503;UBERON:0011216!6.94e-14!223;UBERON:0000483!1.26e-13!306;UBERON:0000119!2.44e-13!309;UBERON:0000481!4.62e-13!342;UBERON:0002619!1.14e-12!22;UBERON:0000956!6.33e-12!25;UBERON:0000203!6.33e-12!25;UBERON:0003056!1.15e-11!61;UBERON:0001950!1.95e-11!20;UBERON:0000064!2.15e-08!218
|ontology_enrichment_uberon=UBERON:0000468!2.09e-25!656;UBERON:0000477!3.98e-22!373;UBERON:0000467!2.06e-21!624;UBERON:0000480!5.62e-21!625;UBERON:0004111!8.80e-21!240;UBERON:0001049!5.58e-20!56;UBERON:0005068!5.58e-20!56;UBERON:0006241!5.58e-20!56;UBERON:0007135!5.58e-20!56;UBERON:0000073!1.52e-18!53;UBERON:0002616!1.52e-18!53;UBERON:0000922!2.77e-18!592;UBERON:0001017!2.43e-17!81;UBERON:0002780!3.90e-17!41;UBERON:0001890!3.90e-17!41;UBERON:0003080!3.90e-17!41;UBERON:0006240!3.90e-17!41;UBERON:0004121!1.35e-16!171;UBERON:0000924!1.35e-16!171;UBERON:0006601!1.35e-16!171;UBERON:0001016!1.77e-16!89;UBERON:0003528!2.35e-16!34;UBERON:0002020!2.35e-16!34;UBERON:0002346!4.61e-16!86;UBERON:0005423!4.89e-16!581;UBERON:0002050!7.44e-16!564;UBERON:0010371!8.73e-16!104;UBERON:0003075!1.10e-15!82;UBERON:0007284!1.10e-15!82;UBERON:0001893!1.24e-15!34;UBERON:0000955!2.61e-15!68;UBERON:0006238!2.61e-15!68;UBERON:0002791!2.75e-15!32;UBERON:0007023!3.32e-15!114;UBERON:0000923!3.35e-15!560;UBERON:0010316!3.35e-15!560;UBERON:0005291!3.35e-15!560;UBERON:0006598!3.35e-15!560;UBERON:0010317!3.35e-15!560;UBERON:0002532!3.35e-15!560;UBERON:0000025!4.03e-15!192;UBERON:0001869!5.90e-15!32;UBERON:0010314!3.54e-14!132;UBERON:0000062!6.07e-14!503;UBERON:0011216!6.94e-14!223;UBERON:0000483!1.26e-13!306;UBERON:0000119!2.44e-13!309;UBERON:0000481!4.62e-13!342;UBERON:0002619!1.14e-12!22;UBERON:0000956!6.33e-12!25;UBERON:0000203!6.33e-12!25;UBERON:0003056!1.15e-11!61;UBERON:0001950!1.95e-11!20;UBERON:0000064!2.15e-08!218
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}}
}}

Revision as of 14:40, 26 November 2012


Full id: C1073_olfactory_Prostate_Cardiac_medial_occipital_seminal_diencephalon



Phase1 CAGE Peaks

Hg19::chr21:27423339..27423352,-p10@APP
Hg19::chr21:27423360..27423381,-p9@APP
Hg19::chr21:27423414..27423442,-p2@APP
Hg19::chr21:27423459..27423508,-p5@APP
Hg19::chr21:27425581..27425626,-p6@APP
Hg19::chr21:27425640..27425676,-p7@APP
Hg19::chr21:27462289..27462323,-p4@APP
Hg19::chr21:27484338..27484350,-p18@APP


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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
epithelial cell1.42e-09253
embryonic cell9.71e-08250
lining cell7.76e-0758
barrier cell7.76e-0758
Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.09e-25656
anatomical cluster3.98e-22373
anatomical system2.06e-21624
anatomical group5.62e-21625
anatomical conduit8.80e-21240
neural tube5.58e-2056
neural rod5.58e-2056
future spinal cord5.58e-2056
neural keel5.58e-2056
regional part of nervous system1.52e-1853
regional part of brain1.52e-1853
embryo2.77e-18592
central nervous system2.43e-1781
regional part of forebrain3.90e-1741
forebrain3.90e-1741
anterior neural tube3.90e-1741
future forebrain3.90e-1741
ectoderm-derived structure1.35e-16171
ectoderm1.35e-16171
presumptive ectoderm1.35e-16171
nervous system1.77e-1689
brain grey matter2.35e-1634
gray matter2.35e-1634
neurectoderm4.61e-1686
developing anatomical structure4.89e-16581
embryonic structure7.44e-16564
ecto-epithelium8.73e-16104
neural plate1.10e-1582
presumptive neural plate1.10e-1582
telencephalon1.24e-1534
brain2.61e-1568
future brain2.61e-1568
regional part of telencephalon2.75e-1532
adult organism3.32e-15114
germ layer3.35e-15560
germ layer / neural crest3.35e-15560
embryonic tissue3.35e-15560
presumptive structure3.35e-15560
germ layer / neural crest derived structure3.35e-15560
epiblast (generic)3.35e-15560
tube4.03e-15192
cerebral hemisphere5.90e-1532
structure with developmental contribution from neural crest3.54e-14132
organ6.07e-14503
organ system subdivision6.94e-14223
epithelium1.26e-13306
cell layer2.44e-13309
multi-tissue structure4.62e-13342
regional part of cerebral cortex1.14e-1222
cerebral cortex6.33e-1225
pallium6.33e-1225
pre-chordal neural plate1.15e-1161
neocortex1.95e-1120
organ part2.15e-08218


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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