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Coexpression cluster:C4828: Difference between revisions

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|full_id=C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid
|full_id=C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid
|id=C4828
|id=C4828
|ontology_enrichment_celltype=CL:0002149!8.83e-08!6;CL:0002255!8.83e-08!6
|ontology_enrichment_celltype=CL:0002149!8.34e-08!6;CL:0002255!8.34e-08!6
|ontology_enrichment_disease=DOID:305!6.43e-21!106;DOID:0050687!4.11e-16!143;DOID:299!1.87e-14!25;DOID:14566!3.95e-08!239;DOID:3001!8.83e-08!6;DOID:162!1.23e-07!235
|ontology_enrichment_disease=DOID:305!2.21e-17!106;DOID:0050687!8.07e-11!143;DOID:299!9.16e-10!25;DOID:3001!8.34e-08!6
|ontology_enrichment_uberon=UBERON:0002619!2.04e-30!22;UBERON:0001893!1.86e-28!34;UBERON:0001869!2.05e-28!32;UBERON:0002791!3.50e-27!33;UBERON:0001950!6.24e-27!20;UBERON:0000956!4.11e-26!25;UBERON:0000203!4.11e-26!25;UBERON:0002780!3.87e-24!41;UBERON:0001890!3.87e-24!41;UBERON:0006240!3.87e-24!41;UBERON:0002020!3.95e-24!34;UBERON:0003528!3.95e-24!34;UBERON:0003080!2.24e-23!42;UBERON:0001737!1.11e-16!9;UBERON:0001049!2.19e-16!57;UBERON:0005068!2.19e-16!57;UBERON:0006241!2.19e-16!57;UBERON:0007135!2.19e-16!57;UBERON:0002616!1.47e-15!59;UBERON:0003056!6.87e-15!61;UBERON:0000955!3.10e-14!69;UBERON:0006238!3.10e-14!69;UBERON:0007023!5.28e-14!115;UBERON:0001017!8.82e-12!82;UBERON:0002346!1.03e-11!90;UBERON:0001871!2.03e-11!7;UBERON:0000200!4.64e-11!6;UBERON:0005743!7.43e-11!86;UBERON:0000073!1.38e-10!94;UBERON:0001016!1.38e-10!94;UBERON:0000349!4.25e-10!5;UBERON:0003075!4.67e-10!86;UBERON:0007284!4.67e-10!86;UBERON:0002108!6.79e-10!14;UBERON:0001557!1.19e-09!19;UBERON:0004921!2.21e-09!129;UBERON:0004185!2.21e-09!129;UBERON:0001007!2.45e-09!155;UBERON:0001555!2.45e-09!155;UBERON:0007026!2.45e-09!155;UBERON:0000062!4.32e-09!511;UBERON:0000064!5.23e-09!219;UBERON:0004119!8.43e-09!169;UBERON:0000925!8.43e-09!169;UBERON:0006595!8.43e-09!169;UBERON:0000160!8.90e-09!27;UBERON:0000481!1.08e-08!347;UBERON:0002021!2.71e-08!5;UBERON:0002075!1.14e-07!18;UBERON:0002114!1.26e-07!12;UBERON:0005409!2.82e-07!35;UBERON:0002771!8.83e-07!3
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}}
}}

Revision as of 16:16, 19 October 2012


Full id: C4828_large_medial_gastric_papillary_embryonic_hippocampus_endometrioid



Phase1 CAGE Peaks

Hg19::chr9:74838100..74838111,+p@chr9:74838100..74838111
+
Hg19::chr9:74864446..74864464,+p9@GDA
Hg19::chr9:74865515..74865533,+p7@GDA


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell of uterus8.34e-086
stromal cell of endometrium8.34e-086
Uber Anatomy
Ontology termp-valuen
cerebral hemisphere1.21e-3532
regional part of cerebral cortex2.41e-3522
telencephalon3.00e-3334
regional part of telencephalon2.05e-3232
cerebral cortex1.09e-3025
pallium1.09e-3025
neocortex3.00e-3020
brain grey matter3.18e-3034
gray matter3.18e-3034
regional part of forebrain1.12e-2641
forebrain1.12e-2641
anterior neural tube1.12e-2641
future forebrain1.12e-2641
larynx8.77e-259
regional part of nervous system2.08e-1953
regional part of brain2.08e-1953
neural tube4.49e-1856
neural rod4.49e-1856
future spinal cord4.49e-1856
neural keel4.49e-1856
gyrus8.37e-176
pre-chordal neural plate3.83e-1661
brain3.81e-1568
future brain3.81e-1568
adult organism3.90e-15114
limbic system5.66e-155
organ system subdivision1.39e-13223
central nervous system3.29e-1381
nervous system1.91e-1289
upper respiratory tract9.39e-1119
temporal lobe1.14e-106
neural plate1.24e-1082
presumptive neural plate1.24e-1082
neurectoderm6.80e-1086
organ part1.98e-09218
frontal cortex2.59e-093
parietal lobe6.38e-095
basal ganglion4.19e-089
nuclear complex of neuraxis4.19e-089
aggregate regional part of brain4.19e-089
collection of basal ganglia4.19e-089
cerebral subcortex4.19e-089
anatomical cluster4.23e-08373
organ1.17e-07503
multi-tissue structure1.54e-07342
internal genitalia2.20e-0725
ecto-epithelium2.63e-07104
amygdala2.90e-072
middle temporal gyrus3.08e-072
Ammon's horn3.90e-072
lobe parts of cerebral cortex3.90e-072
hippocampal formation3.90e-072
limbic lobe3.90e-072
corpus striatum4.17e-074
striatum4.17e-074
ventral part of telencephalon4.17e-074
future corpus striatum4.17e-074
middle frontal gyrus7.20e-072
structure with developmental contribution from neural crest8.15e-07132
Disease
Ontology termp-valuen
carcinoma2.21e-17106
cell type cancer8.07e-11143
adenocarcinoma9.16e-1025
female reproductive endometrioid cancer8.34e-086


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.