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Coexpression cluster:C4313: Difference between revisions

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|full_id=C4313_normal_Lens_Ciliary_Chondrocyte_Mammary_large_Iris
|full_id=C4313_normal_Lens_Ciliary_Chondrocyte_Mammary_large_Iris
|id=C4313
|id=C4313
|ontology_enrichment_celltype=CL:0000066!5.70e-12!254;CL:0002321!1.64e-10!248;CL:0000220!2.05e-10!246;CL:0000055!1.03e-08!180;CL:1000497!1.69e-08!18;CL:0002518!1.69e-08!18;CL:1000449!1.71e-07!16
|ontology_enrichment_celltype=CL:0000066!6.80e-12!253;CL:1000497!8.66e-10!17;CL:0002518!8.66e-10!17;CL:1000449!9.68e-09!15;CL:0002321!1.62e-08!250;CL:1000507!4.69e-08!10;CL:1000494!4.69e-08!10;CL:0002681!9.62e-07!12;CL:0002584!9.62e-07!12
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!8.66e-22!347;UBERON:0000475!1.61e-15!365;UBERON:0000468!1.98e-14!659;UBERON:0003104!6.06e-14!238;UBERON:0009142!6.06e-14!238;UBERON:0000467!2.05e-13!625;UBERON:0000480!4.03e-13!626;UBERON:0000119!2.79e-12!312;UBERON:0000062!5.41e-12!511;UBERON:0000922!5.83e-12!612;UBERON:0000483!1.15e-11!309;UBERON:0000064!4.92e-11!219;UBERON:0002050!5.69e-11!605;UBERON:0005423!5.69e-11!605;UBERON:0000923!1.02e-10!604;UBERON:0005291!1.02e-10!604;UBERON:0006598!1.02e-10!604;UBERON:0002532!1.02e-10!604;UBERON:0001048!1.54e-10!168;UBERON:0005085!6.89e-10!29;UBERON:0001008!7.65e-10!45;UBERON:0000477!7.93e-10!286;UBERON:0006554!8.32e-10!44;UBERON:0004119!1.33e-09!169;UBERON:0000925!1.33e-09!169;UBERON:0006595!1.33e-09!169;UBERON:0001801!6.81e-09!14;UBERON:0003887!7.52e-09!21;UBERON:0000970!7.71e-09!20;UBERON:0002104!9.01e-09!21;UBERON:0000019!9.12e-09!19;UBERON:0000047!9.12e-09!19;UBERON:0004088!9.12e-09!19;UBERON:0003072!9.12e-09!19;UBERON:0003071!9.12e-09!19;UBERON:0004128!9.12e-09!19;UBERON:0001456!1.04e-08!21;UBERON:0000020!1.51e-08!23;UBERON:0005256!1.52e-08!143;UBERON:0001032!1.63e-08!24;UBERON:0004456!1.63e-08!24;UBERON:0003064!1.64e-08!37;UBERON:0001007!2.90e-08!155;UBERON:0001555!2.90e-08!155;UBERON:0007026!2.90e-08!155;UBERON:0002100!3.85e-08!216;UBERON:0004876!7.37e-08!20;UBERON:0002113!8.42e-08!27;UBERON:0003918!8.42e-08!27;UBERON:0005095!8.42e-08!27;UBERON:0007687!8.42e-08!27;UBERON:0000080!1.05e-07!18;UBERON:0002120!1.05e-07!18;UBERON:0004875!1.05e-07!18;UBERON:0005721!1.05e-07!18;UBERON:0005754!1.05e-07!18;UBERON:0007297!1.05e-07!18;UBERON:0006555!1.18e-07!17;UBERON:0005103!1.18e-07!17;UBERON:0000083!1.18e-07!17;UBERON:0009201!1.18e-07!17;UBERON:0004819!1.18e-07!17;UBERON:0006553!1.18e-07!17;UBERON:0003074!1.18e-07!17;UBERON:0003060!1.18e-07!17;UBERON:0004121!1.38e-07!169;UBERON:0005177!1.60e-07!107;UBERON:0004211!1.71e-07!16;UBERON:0001285!1.71e-07!16;UBERON:0007684!1.71e-07!16;UBERON:0003220!1.71e-07!16;UBERON:0004208!1.71e-07!16;UBERON:0000489!2.11e-07!32;UBERON:0007625!2.17e-07!11;UBERON:0001444!3.14e-07!48;UBERON:0000924!3.40e-07!173;UBERON:0006601!3.40e-07!173;UBERON:0004921!6.22e-07!129;UBERON:0004185!6.22e-07!129
|ontology_enrichment_uberon=UBERON:0000481!1.16e-18!342;UBERON:0000477!8.06e-17!373;UBERON:0000467!5.06e-12!624;UBERON:0000480!8.42e-12!625;UBERON:0000468!1.09e-11!656;UBERON:0006554!1.54e-11!47;UBERON:0001008!2.17e-11!48;UBERON:0000062!2.44e-11!503;UBERON:0000119!2.80e-11!309;UBERON:0000483!9.46e-11!306;UBERON:0000064!8.48e-10!218;UBERON:0000475!1.34e-09!264;UBERON:0000922!1.66e-09!592;UBERON:0005085!3.33e-09!31;UBERON:0000970!3.80e-09!21;UBERON:0002104!3.80e-09!21;UBERON:0002113!4.31e-09!26;UBERON:0003918!4.31e-09!26;UBERON:0011143!4.31e-09!26;UBERON:0005095!4.31e-09!26;UBERON:0007687!4.31e-09!26;UBERON:0001801!4.32e-09!14;UBERON:0000019!5.26e-09!20;UBERON:0000047!5.26e-09!20;UBERON:0010312!5.26e-09!20;UBERON:0004088!5.26e-09!20;UBERON:0010230!5.26e-09!20;UBERON:0003072!5.26e-09!20;UBERON:0004128!5.26e-09!20;UBERON:0003071!5.26e-09!20;UBERON:0006555!6.62e-09!16;UBERON:0004819!6.62e-09!16;UBERON:0005423!7.42e-09!581;UBERON:0000020!9.12e-09!24;UBERON:0001032!9.12e-09!24;UBERON:0004456!9.12e-09!24;UBERON:0004211!9.68e-09!15;UBERON:0009773!9.68e-09!15;UBERON:0001231!9.68e-09!15;UBERON:0001285!9.68e-09!15;UBERON:0007684!9.68e-09!15;UBERON:0004208!9.68e-09!15;UBERON:0001456!1.43e-08!22;UBERON:0000489!1.95e-08!31;UBERON:0001048!2.65e-08!160;UBERON:0004119!3.21e-08!160;UBERON:0000925!3.21e-08!160;UBERON:0006595!3.21e-08!160;UBERON:0004810!4.69e-08!10;UBERON:0007625!5.88e-08!11;UBERON:0011216!6.27e-08!223;UBERON:0004121!1.61e-07!171;UBERON:0000924!1.61e-07!171;UBERON:0006601!1.61e-07!171;UBERON:0001007!4.31e-07!145;UBERON:0001555!4.31e-07!145;UBERON:0007026!4.31e-07!145;UBERON:0003104!5.08e-07!160;UBERON:0009142!5.08e-07!160;UBERON:0005172!6.12e-07!54;UBERON:0005173!6.12e-07!54;UBERON:0005177!8.10e-07!101;UBERON:0010371!8.26e-07!104;UBERON:0001225!9.62e-07!12;UBERON:0008987!9.62e-07!12
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285288808649405!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280472854835264!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326639133804138!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739619777817163!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666381359066888!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309993601332744!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330465984872596!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109723399055229
|tf_chipseq_enrich=BHLHE40#8553;3:44.8718135469774:1.10603738662898e-05:0.000285288808649405!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280472854835264!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326639133804138!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000739619777817163!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00666381359066888!SMC3#9126;3:15.0449328449328:0.000293582542037187:0.00309993601332744!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330465984872596!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109723399055229
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}}
}}

Revision as of 15:51, 19 October 2012


Full id: C4313_normal_Lens_Ciliary_Chondrocyte_Mammary_large_Iris



Phase1 CAGE Peaks

Hg19::chr3:189838653..189838658,-p3@LEPREL1
Hg19::chr3:189838670..189838704,-p1@LEPREL1
Hg19::chr3:189838746..189838757,-p4@LEPREL1


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>

Cell Type
Ontology termp-valuen
epithelial cell6.80e-12253
kidney cell8.66e-1017
kidney epithelial cell8.66e-1017
epithelial cell of nephron9.68e-0915
embryonic cell1.62e-08250
kidney tubule cell4.69e-0810
nephron tubule epithelial cell4.69e-0810
kidney cortical cell9.62e-0712
renal cortical epithelial cell9.62e-0712
Uber Anatomy
Ontology termp-valuen
multi-tissue structure1.16e-18342
anatomical cluster8.06e-17373
anatomical system5.06e-12624
anatomical group8.42e-12625
multi-cellular organism1.09e-11656
urinary system structure1.54e-1147
renal system2.17e-1148
organ2.44e-11503
cell layer2.80e-11309
epithelium9.46e-11306
organ part8.48e-10218
organism subdivision1.34e-09264
embryo1.66e-09592
ectodermal placode3.33e-0931
eye3.80e-0921
visual system3.80e-0921
kidney4.31e-0926
kidney mesenchyme4.31e-0926
upper urinary tract4.31e-0926
kidney rudiment4.31e-0926
kidney field4.31e-0926
anterior segment of eyeball4.32e-0914
camera-type eye5.26e-0920
simple eye5.26e-0920
immature eye5.26e-0920
ocular region5.26e-0920
eyeball of camera-type eye5.26e-0920
optic cup5.26e-0920
optic vesicle5.26e-0920
eye primordium5.26e-0920
excretory tube6.62e-0916
kidney epithelium6.62e-0916
developing anatomical structure7.42e-09581
sense organ9.12e-0924
sensory system9.12e-0924
entire sense organ system9.12e-0924
nephron epithelium9.68e-0915
renal tubule9.68e-0915
nephron tubule9.68e-0915
nephron9.68e-0915
uriniferous tubule9.68e-0915
nephrogenic mesenchyme9.68e-0915
face1.43e-0822
cavitated compound organ1.95e-0831
primordium2.65e-08160
endoderm-derived structure3.21e-08160
endoderm3.21e-08160
presumptive endoderm3.21e-08160
nephron tubule epithelium4.69e-0810
pigment epithelium of eye5.88e-0811
organ system subdivision6.27e-08223
ectoderm-derived structure1.61e-07171
ectoderm1.61e-07171
presumptive ectoderm1.61e-07171
digestive system4.31e-07145
digestive tract4.31e-07145
primitive gut4.31e-07145
mesenchyme5.08e-07160
entire embryonic mesenchyme5.08e-07160
abdomen element6.12e-0754
abdominal segment element6.12e-0754
trunk region element8.10e-07101
ecto-epithelium8.26e-07104
cortex of kidney9.62e-0712
renal parenchyma9.62e-0712


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285288808649405
CTCF#1066435.360256373075030.0064925092527670.0280472854835264
E2F1#186934.907389214879320.008460985347239390.0326639133804138
NANOG#79923329.24477848101273.99627955670032e-050.000739619777817163
RAD21#5885310.35503389545630.0009004912073565420.00666381359066888
SMC3#9126315.04493284493280.0002935825420371870.00309993601332744
YY1#752834.911170749853860.008441455341808260.0330465984872596
ZNF263#1012738.221841637010680.001799043925565870.0109723399055229



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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