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Coexpression cluster:C4629: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.12e-52!115;UBERON:0005743!2.04e-21!86;UBERON:0001017!2.11e-21!82;UBERON:0000073!4.23e-21!94;UBERON:0001016!4.23e-21!94;UBERON:0001049!1.59e-20!57;UBERON:0005068!1.59e-20!57;UBERON:0006241!1.59e-20!57;UBERON:0007135!1.59e-20!57;UBERON:0004111!5.18e-19!241;UBERON:0002616!2.21e-18!59;UBERON:0003080!2.94e-18!42;UBERON:0000955!4.07e-18!69;UBERON:0006238!4.07e-18!69;UBERON:0002780!1.20e-17!41;UBERON:0001890!1.20e-17!41;UBERON:0006240!1.20e-17!41;UBERON:0003075!2.79e-16!86;UBERON:0007284!2.79e-16!86;UBERON:0002346!3.07e-16!90;UBERON:0000025!6.95e-16!194;UBERON:0000477!4.42e-15!286;UBERON:0002020!5.51e-15!34;UBERON:0003528!5.51e-15!34;UBERON:0001893!6.70e-15!34;UBERON:0001869!1.37e-14!32;UBERON:0002791!2.58e-14!33;UBERON:0003056!2.59e-14!61;UBERON:0000924!1.81e-13!173;UBERON:0006601!1.81e-13!173;UBERON:0004121!2.63e-13!169;UBERON:0000033!2.64e-13!123;UBERON:0000153!3.01e-13!129;UBERON:0007811!3.01e-13!129;UBERON:0002619!1.36e-12!22;UBERON:0000956!7.53e-12!25;UBERON:0000203!7.53e-12!25;UBERON:0001950!1.12e-11!20;UBERON:0000922!5.52e-11!612;UBERON:0000468!1.15e-10!659;UBERON:0000483!1.54e-10!309;UBERON:0000119!1.69e-10!312;UBERON:0000481!1.88e-09!347;UBERON:0002050!2.61e-09!605;UBERON:0005423!2.61e-09!605;UBERON:0000923!5.00e-09!604;UBERON:0005291!5.00e-09!604;UBERON:0006598!5.00e-09!604;UBERON:0002532!5.00e-09!604;UBERON:0000480!5.36e-09!626;UBERON:0000467!6.61e-09!625;UBERON:0004921!1.25e-08!129;UBERON:0004185!1.25e-08!129;UBERON:0001007!1.02e-07!155;UBERON:0001555!1.02e-07!155;UBERON:0007026!1.02e-07!155;UBERON:0000064!1.23e-07!219;UBERON:0004119!1.60e-07!169;UBERON:0000925!1.60e-07!169;UBERON:0006595!1.60e-07!169
|ontology_enrichment_uberon=UBERON:0007023!4.12e-52!115;UBERON:0005743!2.04e-21!86;UBERON:0001017!2.11e-21!82;UBERON:0000073!4.23e-21!94;UBERON:0001016!4.23e-21!94;UBERON:0001049!1.59e-20!57;UBERON:0005068!1.59e-20!57;UBERON:0006241!1.59e-20!57;UBERON:0007135!1.59e-20!57;UBERON:0004111!5.18e-19!241;UBERON:0002616!2.21e-18!59;UBERON:0003080!2.94e-18!42;UBERON:0000955!4.07e-18!69;UBERON:0006238!4.07e-18!69;UBERON:0002780!1.20e-17!41;UBERON:0001890!1.20e-17!41;UBERON:0006240!1.20e-17!41;UBERON:0003075!2.79e-16!86;UBERON:0007284!2.79e-16!86;UBERON:0002346!3.07e-16!90;UBERON:0000025!6.95e-16!194;UBERON:0000477!4.42e-15!286;UBERON:0002020!5.51e-15!34;UBERON:0003528!5.51e-15!34;UBERON:0001893!6.70e-15!34;UBERON:0001869!1.37e-14!32;UBERON:0002791!2.58e-14!33;UBERON:0003056!2.59e-14!61;UBERON:0000924!1.81e-13!173;UBERON:0006601!1.81e-13!173;UBERON:0004121!2.63e-13!169;UBERON:0000033!2.64e-13!123;UBERON:0000153!3.01e-13!129;UBERON:0007811!3.01e-13!129;UBERON:0002619!1.36e-12!22;UBERON:0000956!7.53e-12!25;UBERON:0000203!7.53e-12!25;UBERON:0001950!1.12e-11!20;UBERON:0000922!5.52e-11!612;UBERON:0000468!1.15e-10!659;UBERON:0000483!1.54e-10!309;UBERON:0000119!1.69e-10!312;UBERON:0000481!1.88e-09!347;UBERON:0002050!2.61e-09!605;UBERON:0005423!2.61e-09!605;UBERON:0000923!5.00e-09!604;UBERON:0005291!5.00e-09!604;UBERON:0006598!5.00e-09!604;UBERON:0002532!5.00e-09!604;UBERON:0000480!5.36e-09!626;UBERON:0000467!6.61e-09!625;UBERON:0004921!1.25e-08!129;UBERON:0004185!1.25e-08!129;UBERON:0001007!1.02e-07!155;UBERON:0001555!1.02e-07!155;UBERON:0007026!1.02e-07!155;UBERON:0000064!1.23e-07!219;UBERON:0004119!1.60e-07!169;UBERON:0000925!1.60e-07!169;UBERON:0006595!1.60e-07!169
|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0226001013976674!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.024691154204406!MAFF#23764;2:37.5435709932968:0.000934477401556032:0.0067718488302186!MAFK#7975;2:18.0671554252199:0.00398367474493681:0.0191182339254873!RXRA#6256;2:13.3830780927555:0.00719643442946573:0.0298391462354681!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370899505623266
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}}
}}

Revision as of 14:15, 5 September 2012


Full id: C4629_salivary_parotid_submaxillary_Whole_stomach_thyroid_breast



Phase1 CAGE Peaks

Hg19::chr6:80341003..80341025,+p2@SH3BGRL2
Hg19::chr6:80341039..80341052,+p1@SH3BGRL2
Hg19::chr6:80411337..80411340,+p6@SH3BGRL2


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 organism4.12e-52115
central nervous system2.11e-2182
regional part of nervous system4.23e-2194
nervous system4.23e-2194
neural tube1.59e-2057
neural rod1.59e-2057
future spinal cord1.59e-2057
neural keel1.59e-2057
anatomical conduit5.18e-19241
regional part of brain2.21e-1859
anterior neural tube2.94e-1842
brain4.07e-1869
future brain4.07e-1869
regional part of forebrain1.20e-1741
forebrain1.20e-1741
future forebrain1.20e-1741
neural plate2.79e-1686
presumptive neural plate2.79e-1686
neurectoderm3.07e-1690
tube6.95e-16194
anatomical cluster4.42e-15286
gray matter5.51e-1534
brain grey matter5.51e-1534
telencephalon6.70e-1534
cerebral hemisphere1.37e-1432
regional part of telencephalon2.58e-1433
pre-chordal neural plate2.59e-1461
ectoderm1.81e-13173
presumptive ectoderm1.81e-13173
ectoderm-derived structure2.63e-13169
head2.64e-13123
anterior region of body3.01e-13129
craniocervical region3.01e-13129
regional part of cerebral cortex1.36e-1222
cerebral cortex7.53e-1225
pallium7.53e-1225
neocortex1.12e-1120
embryo5.52e-11612
multi-cellular organism1.15e-10659
epithelium1.54e-10309
cell layer1.69e-10312
multi-tissue structure1.88e-09347
embryonic structure2.61e-09605
developing anatomical structure2.61e-09605
germ layer5.00e-09604
embryonic tissue5.00e-09604
presumptive structure5.00e-09604
epiblast (generic)5.00e-09604
anatomical group5.36e-09626
anatomical system6.61e-09625
subdivision of digestive tract1.25e-08129
endodermal part of digestive tract1.25e-08129
digestive system1.02e-07155
digestive tract1.02e-07155
primitive gut1.02e-07155
organ part1.23e-07219
endoderm-derived structure1.60e-07169
endoderm1.60e-07169
presumptive endoderm1.60e-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
FOXA2#3170216.42030916844350.004810682352105480.0226001013976674
HNF4A#3172215.42152690863580.005444210486686610.024691154204406
MAFF#23764237.54357099329680.0009344774015560320.0067718488302186
MAFK#7975218.06715542521990.003983674744936810.0191182339254873
RXRA#6256213.38307809275550.007196434429465730.0298391462354681
SIX5#147912211.3911435703060.009873820081429030.0370899505623266



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.