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Coexpression cluster:C3459: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!3.79e-17!143;DOID:305!4.80e-15!106;DOID:14566!1.10e-10!239;DOID:162!5.16e-10!235
|ontology_enrichment_disease=DOID:0050687!3.79e-17!143;DOID:305!4.80e-15!106;DOID:14566!1.10e-10!239;DOID:162!5.16e-10!235
|ontology_enrichment_uberon=UBERON:0000073!1.56e-21!94;UBERON:0001016!1.56e-21!94;UBERON:0005743!1.45e-20!86;UBERON:0001017!3.16e-20!82;UBERON:0001049!1.28e-18!57;UBERON:0005068!1.28e-18!57;UBERON:0006241!1.28e-18!57;UBERON:0007135!1.28e-18!57;UBERON:0002346!1.10e-17!90;UBERON:0000955!2.52e-17!69;UBERON:0006238!2.52e-17!69;UBERON:0002780!2.97e-17!41;UBERON:0001890!2.97e-17!41;UBERON:0006240!2.97e-17!41;UBERON:0000924!4.07e-17!173;UBERON:0006601!4.07e-17!173;UBERON:0003080!7.00e-17!42;UBERON:0003075!8.94e-17!86;UBERON:0007284!8.94e-17!86;UBERON:0002616!1.68e-16!59;UBERON:0004121!3.05e-16!169;UBERON:0000475!2.85e-15!365;UBERON:0000033!2.98e-15!123;UBERON:0000153!2.10e-14!129;UBERON:0007811!2.10e-14!129;UBERON:0003056!2.36e-14!61;UBERON:0002020!6.17e-14!34;UBERON:0003528!6.17e-14!34;UBERON:0001869!9.86e-14!32;UBERON:0001893!9.96e-14!34;UBERON:0002791!2.52e-13!33;UBERON:0000956!1.32e-10!25;UBERON:0000203!1.32e-10!25;UBERON:0000481!3.10e-10!347;UBERON:0002619!6.27e-10!22;UBERON:0000468!6.99e-10!659;UBERON:0000119!4.75e-09!312;UBERON:0000483!7.38e-09!309;UBERON:0001950!8.14e-09!20;UBERON:0000062!1.62e-08!511;UBERON:0000477!1.76e-08!286;UBERON:0000467!6.49e-08!625;UBERON:0000480!8.78e-08!626;UBERON:0004111!3.71e-07!241;UBERON:0007023!5.15e-07!115;UBERON:0000922!9.90e-07!612
|ontology_enrichment_uberon=UBERON:0000073!1.56e-21!94;UBERON:0001016!1.56e-21!94;UBERON:0005743!1.45e-20!86;UBERON:0001017!3.16e-20!82;UBERON:0001049!1.28e-18!57;UBERON:0005068!1.28e-18!57;UBERON:0006241!1.28e-18!57;UBERON:0007135!1.28e-18!57;UBERON:0002346!1.10e-17!90;UBERON:0000955!2.52e-17!69;UBERON:0006238!2.52e-17!69;UBERON:0002780!2.97e-17!41;UBERON:0001890!2.97e-17!41;UBERON:0006240!2.97e-17!41;UBERON:0000924!4.07e-17!173;UBERON:0006601!4.07e-17!173;UBERON:0003080!7.00e-17!42;UBERON:0003075!8.94e-17!86;UBERON:0007284!8.94e-17!86;UBERON:0002616!1.68e-16!59;UBERON:0004121!3.05e-16!169;UBERON:0000475!2.85e-15!365;UBERON:0000033!2.98e-15!123;UBERON:0000153!2.10e-14!129;UBERON:0007811!2.10e-14!129;UBERON:0003056!2.36e-14!61;UBERON:0002020!6.17e-14!34;UBERON:0003528!6.17e-14!34;UBERON:0001869!9.86e-14!32;UBERON:0001893!9.96e-14!34;UBERON:0002791!2.52e-13!33;UBERON:0000956!1.32e-10!25;UBERON:0000203!1.32e-10!25;UBERON:0000481!3.10e-10!347;UBERON:0002619!6.27e-10!22;UBERON:0000468!6.99e-10!659;UBERON:0000119!4.75e-09!312;UBERON:0000483!7.38e-09!309;UBERON:0001950!8.14e-09!20;UBERON:0000062!1.62e-08!511;UBERON:0000477!1.76e-08!286;UBERON:0000467!6.49e-08!625;UBERON:0000480!8.78e-08!626;UBERON:0004111!3.71e-07!241;UBERON:0007023!5.15e-07!115;UBERON:0000922!9.90e-07!612
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}}
}}

Revision as of 13:12, 5 September 2012


Full id: C3459_lung_pituitary_trachea_testis_medulla_caudate_glassy



Phase1 CAGE Peaks

Hg19::chr14:77843721..77843762,+p1@SAMD15
Hg19::chr15:55790515..55790605,-p3@CCPG1
p3@DYX1C1-CCPG1
p3@DYX1C1
Hg19::chr3:197676750..197676802,-p1@IQCG


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.56e-2194
nervous system1.56e-2194
central nervous system3.16e-2082
neural tube1.28e-1857
neural rod1.28e-1857
future spinal cord1.28e-1857
neural keel1.28e-1857
neurectoderm1.10e-1790
brain2.52e-1769
future brain2.52e-1769
regional part of forebrain2.97e-1741
forebrain2.97e-1741
future forebrain2.97e-1741
ectoderm4.07e-17173
presumptive ectoderm4.07e-17173
anterior neural tube7.00e-1742
neural plate8.94e-1786
presumptive neural plate8.94e-1786
regional part of brain1.68e-1659
ectoderm-derived structure3.05e-16169
organism subdivision2.85e-15365
head2.98e-15123
anterior region of body2.10e-14129
craniocervical region2.10e-14129
pre-chordal neural plate2.36e-1461
gray matter6.17e-1434
brain grey matter6.17e-1434
cerebral hemisphere9.86e-1432
telencephalon9.96e-1434
regional part of telencephalon2.52e-1333
cerebral cortex1.32e-1025
pallium1.32e-1025
multi-tissue structure3.10e-10347
regional part of cerebral cortex6.27e-1022
multi-cellular organism6.99e-10659
cell layer4.75e-09312
epithelium7.38e-09309
neocortex8.14e-0920
organ1.62e-08511
anatomical cluster1.76e-08286
anatomical system6.49e-08625
anatomical group8.78e-08626
anatomical conduit3.71e-07241
adult organism5.15e-07115
embryo9.90e-07612
Disease
Ontology termp-valuen
cell type cancer3.79e-17143
carcinoma4.80e-15106
disease of cellular proliferation1.10e-10239
cancer5.16e-10235


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
E2F1#186934.907389214879320.008460985347239390.0324420606755391
ELF1#199734.258097958807540.01295179875054610.046112801176392
ELK4#2005210.8237877723120.01091284719516480.0401864126164738
GABPB1#255337.067683836182170.002832212825417420.0153834759347707
GTF2B#2959221.29588662288280.002878180589911410.015577255668226
MAX#414936.452555509007120.003721913834265510.01861652102188
MXI1#460139.96157162875930.001011470541259020.00719205963089263
POLR3A#111281113.0440366972480.00882009881003120.0334968108953036
RFX5#5993312.04791082719510.0005717246050312580.00483876385938894
SIN3A#2594235.408884726815140.006318961977991520.0275977949240771
YY1#752834.911170749853860.008441455341808260.0328630541783693



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.