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Difference between revisions of "Coexpression cluster:C2145"

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|ontology_enrichment_disease=DOID:162!2.78e-27!235;DOID:14566!5.52e-26!239;DOID:0050687!5.43e-20!143;DOID:305!8.54e-17!106;DOID:0050686!3.04e-11!137;DOID:2531!1.64e-08!51;DOID:0060083!1.64e-08!51;DOID:8692!7.31e-07!31;DOID:1240!8.16e-07!39
 
|ontology_enrichment_disease=DOID:162!2.78e-27!235;DOID:14566!5.52e-26!239;DOID:0050687!5.43e-20!143;DOID:305!8.54e-17!106;DOID:0050686!3.04e-11!137;DOID:2531!1.64e-08!51;DOID:0060083!1.64e-08!51;DOID:8692!7.31e-07!31;DOID:1240!8.16e-07!39
 
|ontology_enrichment_uberon=UBERON:0003104!6.55e-19!238;UBERON:0009142!6.55e-19!238;UBERON:0002100!6.08e-12!216;UBERON:0001041!6.37e-12!98;UBERON:0000481!7.09e-12!347;UBERON:0005177!1.78e-11!107;UBERON:0000072!2.79e-11!46;UBERON:0000077!1.95e-10!130;UBERON:0004921!3.12e-10!129;UBERON:0004185!3.12e-10!129;UBERON:0004119!7.40e-10!169;UBERON:0000925!7.40e-10!169;UBERON:0006595!7.40e-10!169;UBERON:0008947!8.17e-10!38;UBERON:0003258!8.17e-10!38;UBERON:0009569!2.20e-09!113;UBERON:0001048!2.77e-09!168;UBERON:0000490!5.53e-09!138;UBERON:0001007!6.80e-09!155;UBERON:0001555!6.80e-09!155;UBERON:0007026!6.80e-09!155;UBERON:0003914!1.30e-08!118;UBERON:0005256!1.53e-08!143;UBERON:0000065!2.10e-08!53;UBERON:0000063!4.92e-08!97;UBERON:0005181!1.52e-07!35;UBERON:0000119!1.64e-07!312;UBERON:0000483!1.91e-07!309;UBERON:0001004!2.09e-07!72;UBERON:0003103!2.97e-07!69;UBERON:0005178!4.45e-07!34;UBERON:0002224!4.45e-07!34;UBERON:0004802!6.51e-07!19;UBERON:0000115!6.51e-07!19
 
|ontology_enrichment_uberon=UBERON:0003104!6.55e-19!238;UBERON:0009142!6.55e-19!238;UBERON:0002100!6.08e-12!216;UBERON:0001041!6.37e-12!98;UBERON:0000481!7.09e-12!347;UBERON:0005177!1.78e-11!107;UBERON:0000072!2.79e-11!46;UBERON:0000077!1.95e-10!130;UBERON:0004921!3.12e-10!129;UBERON:0004185!3.12e-10!129;UBERON:0004119!7.40e-10!169;UBERON:0000925!7.40e-10!169;UBERON:0006595!7.40e-10!169;UBERON:0008947!8.17e-10!38;UBERON:0003258!8.17e-10!38;UBERON:0009569!2.20e-09!113;UBERON:0001048!2.77e-09!168;UBERON:0000490!5.53e-09!138;UBERON:0001007!6.80e-09!155;UBERON:0001555!6.80e-09!155;UBERON:0007026!6.80e-09!155;UBERON:0003914!1.30e-08!118;UBERON:0005256!1.53e-08!143;UBERON:0000065!2.10e-08!53;UBERON:0000063!4.92e-08!97;UBERON:0005181!1.52e-07!35;UBERON:0000119!1.64e-07!312;UBERON:0000483!1.91e-07!309;UBERON:0001004!2.09e-07!72;UBERON:0003103!2.97e-07!69;UBERON:0005178!4.45e-07!34;UBERON:0002224!4.45e-07!34;UBERON:0004802!6.51e-07!19;UBERON:0000115!6.51e-07!19
 +
|tf_chipseq_enrich=BCLAF1#9774;2:10.8263238050609:0.0120220381643258:0.0436416282184227!BRCA1#672;2:10.0921153216119:0.013771396990026:0.048460895927805!CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511282157863006!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.010626485539454!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00995031291682237!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101273002735781!ELK4#2005;3:12.176761243851:0.000891263257762061:0.00663548926271827!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0191971495093141!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00389749662702329!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185562850802807!HMGN3#9324;3:6.13391079251294:0.00664069668332472:0.0282861340556201!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0465921645605877!MEF2A#4205;3:14.057423182233:0.000583003885418661:0.00488552858775893!MXI1#4601;3:7.47117872156947:0.00374131473855096:0.0186225893613346!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00885626246974638!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0434735530497539!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794392210606986!SP2#6668;2:13.0767652469223:0.00833003653661494:0.0328009910586106!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321269408782133!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140262846666836!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243506076157009!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158566144103013!TFAP2C#7022;3:8.10692145739517:0.00294701173986644:0.015714436796687!THAP1#55145;2:15.6845723014257:0.00584046967835792:0.0262421619660137!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00506998477667676!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106617503532146!ZBTB33#10009;2:15.8323625149906:0.00573424893032464:0.0258349175632706!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342248841695692!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000619647883620676
 
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}}
 
}}

Revision as of 04:48, 5 September 2012


Full id: C2145_Mesenchymal_Alveolar_Renal_Placental_nonsmall_Bronchial_left



Phase1 CAGE Peaks

  Short description
Hg19::chr11:62439136..62439162,+ p1@C11orf83
Hg19::chr17:73900954..73901003,- p1@MRPL38
Hg19::chr17:79670440..79670524,+ p1@MRPL12
p1@SLC25A10
Hg19::chr8:145149957..145150006,+ p1@CYC1


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0005739mitochondrion0.00246685015740525
GO:0045155electron transporter, transferring electrons from CoQH2-cytochrome c reductase complex and cytochrome c oxidase complex activity0.0085656256290494
GO:0006390transcription from mitochondrial promoter0.0142747820013017
GO:0044429mitochondrial part0.0214058702371865
GO:0000315organellar large ribosomal subunit0.0214058702371865
GO:0005762mitochondrial large ribosomal subunit0.0214058702371865
GO:0005840ribosome0.0255028847072952
GO:0044444cytoplasmic part0.0299280631346191
GO:0030529ribonucleoprotein complex0.0354431211698454
GO:0000313organellar ribosome0.0396560987964519
GO:0005761mitochondrial ribosome0.0396560987964519



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data
disease_data


Cell Type
Ontology termp-valuen
epithelial cell3.44e-30254
embryonic cell1.33e-16248
animal cell2.00e-08679
eukaryotic cell2.00e-08679
endodermal cell3.37e-0759
epithelial cell of lung6.51e-0719
Uber Anatomy
Ontology termp-valuen
mesenchyme6.55e-19238
entire embryonic mesenchyme6.55e-19238
trunk6.08e-12216
foregut6.37e-1298
multi-tissue structure7.09e-12347
trunk region element1.78e-11107
segment of respiratory tract2.79e-1146
mixed endoderm/mesoderm-derived structure1.95e-10130
subdivision of digestive tract3.12e-10129
endodermal part of digestive tract3.12e-10129
endoderm-derived structure7.40e-10169
endoderm7.40e-10169
presumptive endoderm7.40e-10169
respiratory primordium8.17e-1038
endoderm of foregut8.17e-1038
subdivision of trunk2.20e-09113
primordium2.77e-09168
unilaminar epithelium5.53e-09138
digestive system6.80e-09155
digestive tract6.80e-09155
primitive gut6.80e-09155
epithelial tube1.30e-08118
trunk mesenchyme1.53e-08143
respiratory tract2.10e-0853
organ segment4.92e-0897
thoracic segment organ1.52e-0735
cell layer1.64e-07312
epithelium1.91e-07309
respiratory system2.09e-0772
compound organ2.97e-0769
thoracic cavity element4.45e-0734
thoracic cavity4.45e-0734
respiratory tract epithelium6.51e-0719
lung epithelium6.51e-0719
Disease
Ontology termp-valuen
cancer2.78e-27235
disease of cellular proliferation5.52e-26239
cell type cancer5.43e-20143
carcinoma8.54e-17106
organ system cancer3.04e-11137
hematologic cancer1.64e-0851
immune system cancer1.64e-0851
myeloid leukemia7.31e-0731
leukemia8.16e-0739


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCLAF1#9774210.82632380506090.01202203816432580.0436416282184227
BRCA1#672210.09211532161190.0137713969900260.048460895927805
CCNT2#90546.336201576962630.0006203100587215640.00511282157863006
E2F1#186944.907389214879320.001724022357361790.010626485539454
E2F6#187645.017155731697390.00157802193473060.00995031291682237
EGR1#195844.988179094810140.001615011500076050.0101273002735781
ELK4#2005312.1767612438510.0008912632577620610.00663548926271827
ETS1#211337.296570691651750.00400857377511390.0191971495093141
GABPB1#255347.067683836182170.0004006876864423170.00389749662702329
HEY1#2346244.040111043105710.00375304636917980.0185562850802807
HMGN3#932436.133910792512940.006640696683324720.0282861340556201
MAX#414934.839416631755340.01315737137836840.0465921645605877
MEF2A#4205314.0574231822330.0005830038854186610.00488552858775893
MXI1#460137.471178721569470.003741314738550960.0186225893613346
MYC#460945.22228187160940.001344309395272740.00885626246974638
PAX5#507935.002174148383370.01196533174786410.0434735530497539
SIN3A#2594245.408884726815140.001168172384885160.00794392210606986
SP2#6668213.07676524692230.008330036536614940.0328009910586106
TAF1#687243.343046285745290.008005664898701650.0321269408782133
TAF7#687938.574802053692940.00250055433515240.0140262846666836
TBP#690843.706770687096390.005296377814784350.0243506076157009
TCF7L2#693438.077632422353010.002978381685834620.0158566144103013
TFAP2C#702238.106921457395170.002947011739866440.015714436796687
THAP1#55145215.68457230142570.005840469678357920.0262421619660137
USF1#739146.361499277207960.0006105011399140830.00506998477667676
YY1#752844.911170749853860.00171871838055440.0106617503532146
ZBTB33#10009215.83236251499060.005734248930324640.0258349175632706
ZBTB7A#5134135.513931980906920.009038352821081090.0342248841695692
ZNF143#7702413.50087655222793.00867915035614e-050.000619647883620676



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.