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Coexpression cluster:C3617: Difference between revisions

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|full_id=C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis
|full_id=C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis
|id=C3617
|id=C3617
|ontology_enrichment_celltype=CL:0000055!9.45e-07!180
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.54e-35!365;UBERON:0002346!3.47e-28!90;UBERON:0003075!1.04e-27!86;UBERON:0007284!1.04e-27!86;UBERON:0000924!8.97e-26!173;UBERON:0006601!8.97e-26!173;UBERON:0000481!1.09e-25!347;UBERON:0001049!1.15e-25!57;UBERON:0005068!1.15e-25!57;UBERON:0006241!1.15e-25!57;UBERON:0007135!1.15e-25!57;UBERON:0004121!4.31e-25!169;UBERON:0005743!5.72e-25!86;UBERON:0000483!7.54e-24!309;UBERON:0000033!7.74e-24!123;UBERON:0000153!8.18e-24!129;UBERON:0007811!8.18e-24!129;UBERON:0000119!9.14e-24!312;UBERON:0002616!1.19e-23!59;UBERON:0001017!2.17e-23!82;UBERON:0000955!2.20e-23!69;UBERON:0006238!2.20e-23!69;UBERON:0000073!5.53e-23!94;UBERON:0001016!5.53e-23!94;UBERON:0003056!1.32e-21!61;UBERON:0000477!5.22e-21!286;UBERON:0007023!6.58e-20!115;UBERON:0000468!7.52e-20!659;UBERON:0002780!8.53e-20!41;UBERON:0001890!8.53e-20!41;UBERON:0006240!8.53e-20!41;UBERON:0000064!8.76e-19!219;UBERON:0003080!9.31e-19!42;UBERON:0004111!1.55e-18!241;UBERON:0000025!4.46e-18!194;UBERON:0001893!3.03e-16!34;UBERON:0002020!4.01e-16!34;UBERON:0003528!4.01e-16!34;UBERON:0001869!9.04e-16!32;UBERON:0002791!1.23e-15!33;UBERON:0000062!1.02e-14!511;UBERON:0000467!1.23e-14!625;UBERON:0000480!2.34e-14!626;UBERON:0000922!2.71e-14!612;UBERON:0002050!5.14e-14!605;UBERON:0005423!5.14e-14!605;UBERON:0000923!9.82e-14!604;UBERON:0005291!9.82e-14!604;UBERON:0006598!9.82e-14!604;UBERON:0002532!9.82e-14!604;UBERON:0002619!1.93e-12!22;UBERON:0000956!4.14e-12!25;UBERON:0000203!4.14e-12!25;UBERON:0001950!1.78e-11!20;UBERON:0003076!4.32e-08!15;UBERON:0003057!4.32e-08!15;UBERON:0000063!1.63e-07!97;UBERON:0002100!3.09e-07!216;UBERON:0004732!3.50e-07!13;UBERON:0004733!6.11e-07!12;UBERON:0002028!6.11e-07!12;UBERON:0007277!6.11e-07!12
|ontology_enrichment_uberon=UBERON:0000477!1.40e-26!373;UBERON:0000481!3.85e-26!342;UBERON:0002346!4.19e-26!86;UBERON:0003075!1.98e-25!82;UBERON:0007284!1.98e-25!82;UBERON:0001049!9.47e-25!56;UBERON:0005068!9.47e-25!56;UBERON:0006241!9.47e-25!56;UBERON:0007135!9.47e-25!56;UBERON:0004121!9.29e-24!171;UBERON:0000924!9.29e-24!171;UBERON:0006601!9.29e-24!171;UBERON:0000483!1.09e-23!306;UBERON:0000119!1.48e-23!309;UBERON:0000073!1.59e-23!53;UBERON:0002616!1.59e-23!53;UBERON:0010314!1.73e-23!132;UBERON:0010371!2.64e-23!104;UBERON:0000955!6.66e-23!68;UBERON:0006238!6.66e-23!68;UBERON:0001017!9.15e-23!81;UBERON:0001016!5.95e-21!89;UBERON:0003056!1.81e-20!61;UBERON:0007023!3.30e-19!114;UBERON:0002780!2.10e-18!41;UBERON:0001890!2.10e-18!41;UBERON:0003080!2.10e-18!41;UBERON:0006240!2.10e-18!41;UBERON:0004111!2.82e-18!240;UBERON:0000468!4.95e-18!656;UBERON:0000025!3.26e-17!192;UBERON:0000064!4.50e-16!218;UBERON:0011216!3.73e-15!223;UBERON:0003528!4.08e-15!34;UBERON:0002020!4.08e-15!34;UBERON:0001893!4.17e-15!34;UBERON:0001869!1.94e-14!32;UBERON:0000467!2.63e-14!624;UBERON:0000480!4.67e-14!625;UBERON:0002791!5.69e-14!32;UBERON:0000062!5.02e-13!503;UBERON:0005423!5.05e-13!581;UBERON:0000922!2.65e-12!592;UBERON:0000475!2.92e-11!264;UBERON:0002619!4.01e-11!22;UBERON:0000956!6.11e-11!25;UBERON:0000203!6.11e-11!25;UBERON:0000923!2.63e-10!560;UBERON:0010316!2.63e-10!560;UBERON:0005291!2.63e-10!560;UBERON:0006598!2.63e-10!560;UBERON:0010317!2.63e-10!560;UBERON:0002532!2.63e-10!560;UBERON:0002050!2.93e-10!564;UBERON:0001950!3.04e-10!20;UBERON:0003076!1.52e-07!15;UBERON:0003057!1.52e-07!15;UBERON:0002100!9.08e-07!199
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461678866073341!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719597900943808!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276301473736427!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370699509484638!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158657907451129
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461678866073341!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00719597900943808!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276301473736427!SIX5#147912;2:11.391143570306:0.00987382008142903:0.0370699509484638!THAP1#55145;2:20.9127630685675:0.00298344741373694:0.0158657907451129
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}}
}}

Revision as of 15:15, 19 October 2012


Full id: C3617_testis_trachea_putamen_pituitary_lung_caudate_epididymis



Phase1 CAGE Peaks

Hg19::chr17:260097..260196,+p1@C17orf97
Hg19::chr1:36916011..36916057,-p1@OSCP1
Hg19::chr9:135753649..135753688,-p1@AK8


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
anatomical cluster1.40e-26373
multi-tissue structure3.85e-26342
neurectoderm4.19e-2686
neural plate1.98e-2582
presumptive neural plate1.98e-2582
neural tube9.47e-2556
neural rod9.47e-2556
future spinal cord9.47e-2556
neural keel9.47e-2556
ectoderm-derived structure9.29e-24171
ectoderm9.29e-24171
presumptive ectoderm9.29e-24171
epithelium1.09e-23306
cell layer1.48e-23309
regional part of nervous system1.59e-2353
regional part of brain1.59e-2353
structure with developmental contribution from neural crest1.73e-23132
ecto-epithelium2.64e-23104
brain6.66e-2368
future brain6.66e-2368
central nervous system9.15e-2381
nervous system5.95e-2189
pre-chordal neural plate1.81e-2061
adult organism3.30e-19114
regional part of forebrain2.10e-1841
forebrain2.10e-1841
anterior neural tube2.10e-1841
future forebrain2.10e-1841
anatomical conduit2.82e-18240
multi-cellular organism4.95e-18656
tube3.26e-17192
organ part4.50e-16218
organ system subdivision3.73e-15223
brain grey matter4.08e-1534
gray matter4.08e-1534
telencephalon4.17e-1534
cerebral hemisphere1.94e-1432
anatomical system2.63e-14624
anatomical group4.67e-14625
regional part of telencephalon5.69e-1432
organ5.02e-13503
developing anatomical structure5.05e-13581
embryo2.65e-12592
organism subdivision2.92e-11264
regional part of cerebral cortex4.01e-1122
cerebral cortex6.11e-1125
pallium6.11e-1125
germ layer2.63e-10560
germ layer / neural crest2.63e-10560
embryonic tissue2.63e-10560
presumptive structure2.63e-10560
germ layer / neural crest derived structure2.63e-10560
epiblast (generic)2.63e-10560
embryonic structure2.93e-10564
neocortex3.04e-1020
posterior neural tube1.52e-0715
chordal neural plate1.52e-0715
trunk9.08e-07199


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
ELF1#199734.258097958807540.01295179875054610.0461678866073341
MXI1#460139.96157162875930.001011470541259020.00719597900943808
SIN3A#2594235.408884726815140.006318961977991520.0276301473736427
SIX5#147912211.3911435703060.009873820081429030.0370699509484638
THAP1#55145220.91276306856750.002983447413736940.0158657907451129



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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