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Coexpression cluster:C4090: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.56e-38!115;UBERON:0004111!6.69e-23!241;UBERON:0000477!6.88e-19!286;UBERON:0000025!2.66e-16!194;UBERON:0000153!2.72e-15!129;UBERON:0007811!2.72e-15!129;UBERON:0001049!3.02e-15!57;UBERON:0005068!3.02e-15!57;UBERON:0006241!3.02e-15!57;UBERON:0007135!3.02e-15!57;UBERON:0003080!7.98e-15!42;UBERON:0003075!8.95e-15!86;UBERON:0007284!8.95e-15!86;UBERON:0005743!1.03e-14!86;UBERON:0000483!1.65e-14!309;UBERON:0002780!3.32e-14!41;UBERON:0001890!3.32e-14!41;UBERON:0006240!3.32e-14!41;UBERON:0003056!4.39e-14!61;UBERON:0000033!6.39e-14!123;UBERON:0000119!7.78e-14!312;UBERON:0000073!1.31e-13!94;UBERON:0001016!1.31e-13!94;UBERON:0002346!2.24e-13!90;UBERON:0001017!4.85e-13!82;UBERON:0000955!1.05e-12!69;UBERON:0006238!1.05e-12!69;UBERON:0002616!2.28e-12!59;UBERON:0000481!3.05e-12!347;UBERON:0000468!4.98e-12!659;UBERON:0004121!1.05e-11!169;UBERON:0001869!1.57e-11!32;UBERON:0000475!2.18e-11!365;UBERON:0001893!3.90e-11!34;UBERON:0002020!3.93e-11!34;UBERON:0003528!3.93e-11!34;UBERON:0000922!5.53e-11!612;UBERON:0000480!5.58e-11!626;UBERON:0000924!6.25e-11!173;UBERON:0006601!6.25e-11!173;UBERON:0000467!6.86e-11!625;UBERON:0002791!1.24e-10!33;UBERON:0002619!2.71e-10!22;UBERON:0002050!9.23e-10!605;UBERON:0005423!9.23e-10!605;UBERON:0001950!1.01e-09!20;UBERON:0001986!1.02e-09!18;UBERON:0004638!1.02e-09!18;UBERON:0004852!1.02e-09!18;UBERON:0000923!1.26e-09!604;UBERON:0005291!1.26e-09!604;UBERON:0006598!1.26e-09!604;UBERON:0002532!1.26e-09!604;UBERON:0000956!1.58e-08!25;UBERON:0000203!1.58e-08!25;UBERON:0000064!2.68e-08!219;UBERON:0000487!2.80e-08!22;UBERON:0004921!5.61e-08!129;UBERON:0004185!5.61e-08!129;UBERON:0006914!7.83e-08!25;UBERON:0001007!1.93e-07!155;UBERON:0001555!1.93e-07!155;UBERON:0007026!1.93e-07!155;UBERON:0002530!6.80e-07!59;UBERON:0001041!7.25e-07!98;UBERON:0009569!7.94e-07!113;UBERON:0004119!8.37e-07!169;UBERON:0000925!8.37e-07!169;UBERON:0006595!8.37e-07!169
|ontology_enrichment_uberon=UBERON:0007023!2.56e-38!115;UBERON:0004111!6.69e-23!241;UBERON:0000477!6.88e-19!286;UBERON:0000025!2.66e-16!194;UBERON:0000153!2.72e-15!129;UBERON:0007811!2.72e-15!129;UBERON:0001049!3.02e-15!57;UBERON:0005068!3.02e-15!57;UBERON:0006241!3.02e-15!57;UBERON:0007135!3.02e-15!57;UBERON:0003080!7.98e-15!42;UBERON:0003075!8.95e-15!86;UBERON:0007284!8.95e-15!86;UBERON:0005743!1.03e-14!86;UBERON:0000483!1.65e-14!309;UBERON:0002780!3.32e-14!41;UBERON:0001890!3.32e-14!41;UBERON:0006240!3.32e-14!41;UBERON:0003056!4.39e-14!61;UBERON:0000033!6.39e-14!123;UBERON:0000119!7.78e-14!312;UBERON:0000073!1.31e-13!94;UBERON:0001016!1.31e-13!94;UBERON:0002346!2.24e-13!90;UBERON:0001017!4.85e-13!82;UBERON:0000955!1.05e-12!69;UBERON:0006238!1.05e-12!69;UBERON:0002616!2.28e-12!59;UBERON:0000481!3.05e-12!347;UBERON:0000468!4.98e-12!659;UBERON:0004121!1.05e-11!169;UBERON:0001869!1.57e-11!32;UBERON:0000475!2.18e-11!365;UBERON:0001893!3.90e-11!34;UBERON:0002020!3.93e-11!34;UBERON:0003528!3.93e-11!34;UBERON:0000922!5.53e-11!612;UBERON:0000480!5.58e-11!626;UBERON:0000924!6.25e-11!173;UBERON:0006601!6.25e-11!173;UBERON:0000467!6.86e-11!625;UBERON:0002791!1.24e-10!33;UBERON:0002619!2.71e-10!22;UBERON:0002050!9.23e-10!605;UBERON:0005423!9.23e-10!605;UBERON:0001950!1.01e-09!20;UBERON:0001986!1.02e-09!18;UBERON:0004638!1.02e-09!18;UBERON:0004852!1.02e-09!18;UBERON:0000923!1.26e-09!604;UBERON:0005291!1.26e-09!604;UBERON:0006598!1.26e-09!604;UBERON:0002532!1.26e-09!604;UBERON:0000956!1.58e-08!25;UBERON:0000203!1.58e-08!25;UBERON:0000064!2.68e-08!219;UBERON:0000487!2.80e-08!22;UBERON:0004921!5.61e-08!129;UBERON:0004185!5.61e-08!129;UBERON:0006914!7.83e-08!25;UBERON:0001007!1.93e-07!155;UBERON:0001555!1.93e-07!155;UBERON:0007026!1.93e-07!155;UBERON:0002530!6.80e-07!59;UBERON:0001041!7.25e-07!98;UBERON:0009569!7.94e-07!113;UBERON:0004119!8.37e-07!169;UBERON:0000925!8.37e-07!169;UBERON:0006595!8.37e-07!169
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}}
}}

Revision as of 11:49, 5 September 2012


Full id: C4090_salivary_Hepatocyte_liver_parotid_submaxillary_tongue_lung



Phase1 CAGE Peaks

Hg19::chr22:25507144..25507210,+p@chr22:25507144..25507210
+
Hg19::chr22:25507901..25507915,+p@chr22:25507901..25507915
+
Hg19::chr22:25507920..25507932,+p@chr22:25507920..25507932
+


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>


Uber Anatomy
Ontology termp-valuen
adult organism2.56e-38115
anatomical conduit6.69e-23241
anatomical cluster6.88e-19286
tube2.66e-16194
anterior region of body2.72e-15129
craniocervical region2.72e-15129
neural tube3.02e-1557
neural rod3.02e-1557
future spinal cord3.02e-1557
neural keel3.02e-1557
anterior neural tube7.98e-1542
neural plate8.95e-1586
presumptive neural plate8.95e-1586
epithelium1.65e-14309
regional part of forebrain3.32e-1441
forebrain3.32e-1441
future forebrain3.32e-1441
pre-chordal neural plate4.39e-1461
head6.39e-14123
cell layer7.78e-14312
regional part of nervous system1.31e-1394
nervous system1.31e-1394
neurectoderm2.24e-1390
central nervous system4.85e-1382
brain1.05e-1269
future brain1.05e-1269
regional part of brain2.28e-1259
multi-tissue structure3.05e-12347
multi-cellular organism4.98e-12659
ectoderm-derived structure1.05e-11169
cerebral hemisphere1.57e-1132
organism subdivision2.18e-11365
telencephalon3.90e-1134
gray matter3.93e-1134
brain grey matter3.93e-1134
embryo5.53e-11612
anatomical group5.58e-11626
ectoderm6.25e-11173
presumptive ectoderm6.25e-11173
anatomical system6.86e-11625
regional part of telencephalon1.24e-1033
regional part of cerebral cortex2.71e-1022
embryonic structure9.23e-10605
developing anatomical structure9.23e-10605
neocortex1.01e-0920
endothelium1.02e-0918
blood vessel endothelium1.02e-0918
cardiovascular system endothelium1.02e-0918
germ layer1.26e-09604
embryonic tissue1.26e-09604
presumptive structure1.26e-09604
epiblast (generic)1.26e-09604
cerebral cortex1.58e-0825
pallium1.58e-0825
organ part2.68e-08219
simple squamous epithelium2.80e-0822
subdivision of digestive tract5.61e-08129
endodermal part of digestive tract5.61e-08129
squamous epithelium7.83e-0825
digestive system1.93e-07155
digestive tract1.93e-07155
primitive gut1.93e-07155
gland6.80e-0759
foregut7.25e-0798
subdivision of trunk7.94e-07113
endoderm-derived structure8.37e-07169
endoderm8.37e-07169
presumptive endoderm8.37e-07169


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
CTCF#1066435.360256373075030.0064925092527670.0279986445556914
FOXA1#3169311.08141974938550.000734755275698670.00582179699861113
FOXA2#3170324.63046375266526.68983856509345e-050.00107357106622587
USF1#739136.361499277207960.00388404057290560.0190667597364836



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.