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Coexpression cluster:C2015: Difference between revisions

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|full_id=C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral
|full_id=C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral
|id=C2015
|id=C2015
|ontology_enrichment_celltype=CL:0000066!1.46e-42!254;CL:0000223!8.34e-19!59;CL:0002076!3.69e-17!43;CL:0002251!7.03e-09!21;CL:0002368!4.43e-07!13
|ontology_enrichment_celltype=CL:0000066!5.87e-49!253;CL:0000223!3.76e-22!58;CL:0002076!3.08e-20!42;CL:0002251!4.98e-11!20;CL:0002368!7.94e-08!13;CL:0000082!2.82e-07!19
|ontology_enrichment_disease=DOID:305!1.17e-36!106;DOID:0050687!2.04e-28!143;DOID:162!9.36e-14!235;DOID:14566!5.31e-13!239;DOID:299!2.63e-10!25;DOID:1749!2.34e-08!14
|ontology_enrichment_disease=DOID:305!8.19e-40!106;DOID:0050687!5.90e-33!143;DOID:162!2.50e-15!235;DOID:14566!6.29e-15!239;DOID:299!1.26e-10!25;DOID:1749!1.58e-10!14
|ontology_enrichment_uberon=UBERON:0004119!4.09e-27!169;UBERON:0000925!4.09e-27!169;UBERON:0006595!4.09e-27!169;UBERON:0001007!7.51e-22!155;UBERON:0001555!7.51e-22!155;UBERON:0007026!7.51e-22!155;UBERON:0004921!6.33e-21!129;UBERON:0004185!6.33e-21!129;UBERON:0000077!4.84e-19!130;UBERON:0001041!5.73e-16!98;UBERON:0000466!3.06e-14!126;UBERON:0001004!7.19e-14!72;UBERON:0005911!2.87e-13!82;UBERON:0001048!3.61e-13!168;UBERON:0000062!8.84e-13!511;UBERON:0000464!9.38e-13!104;UBERON:0005177!1.39e-11!107;UBERON:0000065!3.15e-11!53;UBERON:0008947!2.54e-10!38;UBERON:0003258!2.54e-10!38;UBERON:0000481!2.17e-09!347;UBERON:0005153!3.18e-09!37;UBERON:0000064!1.19e-08!219;UBERON:0000072!1.55e-08!46;UBERON:0005157!3.27e-08!51;UBERON:0005409!3.31e-08!35;UBERON:0000468!4.55e-08!659;UBERON:0000922!6.30e-08!612;UBERON:0002048!2.07e-07!22;UBERON:0000117!2.07e-07!22;UBERON:0000171!2.07e-07!22;UBERON:0000170!2.07e-07!22;UBERON:0005597!2.07e-07!22;UBERON:0000118!2.07e-07!22;UBERON:0000063!2.11e-07!97;UBERON:0002553!2.90e-07!70;UBERON:0009569!4.99e-07!113;UBERON:0003104!5.10e-07!238;UBERON:0009142!5.10e-07!238;UBERON:0002050!6.47e-07!605;UBERON:0005423!6.47e-07!605;UBERON:0005178!8.55e-07!34;UBERON:0002224!8.55e-07!34;UBERON:0005181!8.89e-07!35;UBERON:0000344!8.97e-07!12;UBERON:0000923!9.16e-07!604;UBERON:0005291!9.16e-07!604;UBERON:0006598!9.16e-07!604;UBERON:0002532!9.16e-07!604
|ontology_enrichment_uberon=UBERON:0004119!2.12e-30!160;UBERON:0000925!2.12e-30!160;UBERON:0006595!2.12e-30!160;UBERON:0001007!1.82e-24!145;UBERON:0001555!1.82e-24!145;UBERON:0007026!1.82e-24!145;UBERON:0004921!5.16e-23!118;UBERON:0001041!1.41e-18!87;UBERON:0001004!4.94e-17!74;UBERON:0005911!1.66e-16!82;UBERON:0005177!9.42e-15!101;UBERON:0000466!2.03e-14!117;UBERON:0000065!3.78e-14!54;UBERON:0008947!9.31e-13!38;UBERON:0003258!9.31e-13!38;UBERON:0000464!2.40e-12!95;UBERON:0001048!1.19e-11!160;UBERON:0005153!1.57e-10!37;UBERON:0000072!1.57e-10!47;UBERON:0000062!1.63e-09!503;UBERON:0005157!2.16e-09!47;UBERON:0006554!6.53e-09!47;UBERON:0001008!1.68e-08!48;UBERON:0002048!2.24e-08!22;UBERON:0000117!2.24e-08!22;UBERON:0000171!2.24e-08!22;UBERON:0000170!2.24e-08!22;UBERON:0005597!2.24e-08!22;UBERON:0000118!2.24e-08!22;UBERON:0005178!3.20e-08!34;UBERON:0002224!3.20e-08!34;UBERON:0005181!9.59e-08!35;UBERON:0000063!1.06e-07!98;UBERON:0009569!1.36e-07!112;UBERON:0000064!1.85e-07!218;UBERON:0000475!2.57e-07!264;UBERON:0004802!2.82e-07!19;UBERON:0000115!2.82e-07!19;UBERON:0003929!3.25e-07!54;UBERON:0002530!3.25e-07!59;UBERON:0004807!6.47e-07!28
|tf_chipseq_enrich=CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00139187612181194!E2F1#1869;5:4.90738921487932:0.000351281809925646:0.00353580579672557!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.0032331766899504!EBF1#1879;5:8.906466846569:1.78355672307702e-05:0.000406887026215467!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00573893585761928!FOSL2#2355;5:16.9302006045617:7.18315284751475e-07:3.21285353422524e-05!FOXA1#3169;5:11.0814197493855:5.98116883436141e-06:0.00017934748546996!FOXA2#3170;5:24.6304637526652:1.10174651693954e-07:6.41389657093916e-06!GABPB1#2553;5:7.06768383618217:5.6685482528729e-05:0.000949811504864098!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00675099815905765!HMGN3#9324;5:8.17854772335059:2.73180911341838e-05:0.000582973870037397!MXI1#4601;5:9.9615716287593:1.01894348670516e-05:0.000266844129408225!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276848842501657!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00248390295490323!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135579333671476!TBP#6908;5:3.70677068709639:0.00142875510672112:0.00920529022768953!TCF7L2#6934;5:10.7701765631373:6.89693748574565e-06:0.000200252781227075!USF1#7391;5:6.36149927720796:9.59569864925045e-05:0.00137113855688749!YY1#7528;5:4.91117074985386:0.0003499314082136:0.00353242667141118
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}}
}}

Revision as of 11:58, 19 October 2012


Full id: C2015_small_squamous_amniotic_rectal_malignant_maxillary_oral



Phase1 CAGE Peaks

Hg19::chr8:82644522..82644557,-p4@ZFAND1
Hg19::chr8:82644562..82644654,-p2@ZFAND1
Hg19::chr8:82644655..82644687,-p3@ZFAND1
Hg19::chr8:82644669..82644738,+p1@CHMP4C
Hg19::chr8:82644741..82644791,+p2@CHMP4C


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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell5.87e-49253
endodermal cell3.76e-2258
endo-epithelial cell3.08e-2042
epithelial cell of alimentary canal4.98e-1120
respiratory epithelial cell7.94e-0813
epithelial cell of lung2.82e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.12e-30160
endoderm2.12e-30160
presumptive endoderm2.12e-30160
digestive system1.82e-24145
digestive tract1.82e-24145
primitive gut1.82e-24145
subdivision of digestive tract5.16e-23118
foregut1.41e-1887
respiratory system4.94e-1774
endo-epithelium1.66e-1682
trunk region element9.42e-15101
immaterial anatomical entity2.03e-14117
respiratory tract3.78e-1454
respiratory primordium9.31e-1338
endoderm of foregut9.31e-1338
anatomical space2.40e-1295
primordium1.19e-11160
epithelial bud1.57e-1037
segment of respiratory tract1.57e-1047
organ1.63e-09503
epithelial fold2.16e-0947
urinary system structure6.53e-0947
renal system1.68e-0848
lung2.24e-0822
respiratory tube2.24e-0822
respiration organ2.24e-0822
pair of lungs2.24e-0822
lung primordium2.24e-0822
lung bud2.24e-0822
thoracic cavity element3.20e-0834
thoracic cavity3.20e-0834
thoracic segment organ9.59e-0835
organ segment1.06e-0798
subdivision of trunk1.36e-07112
organ part1.85e-07218
organism subdivision2.57e-07264
respiratory tract epithelium2.82e-0719
lung epithelium2.82e-0719
gut epithelium3.25e-0754
gland3.25e-0759
respiratory system epithelium6.47e-0728
Disease
Ontology termp-valuen
carcinoma8.19e-40106
cell type cancer5.90e-33143
cancer2.50e-15235
disease of cellular proliferation6.29e-15239
adenocarcinoma1.26e-1025
squamous cell carcinoma1.58e-1014


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
CCNT2#90556.336201576962639.78880505817628e-050.00139187612181194
E2F1#186954.907389214879320.0003512818099256460.00353580579672557
E2F6#187655.017155731697390.0003144978599297790.0032331766899504
EBF1#187958.9064668465691.78355672307702e-050.000406887026215467
ELF1#199754.258097958807540.0007142416939776840.00573893585761928
FOSL2#2355516.93020060456177.18315284751475e-073.21285353422524e-05
FOXA1#3169511.08141974938555.98116883436141e-060.00017934748546996
FOXA2#3170524.63046375266521.10174651693954e-076.41389657093916e-06
GABPB1#255357.067683836182175.6685482528729e-050.000949811504864098
HEY1#2346254.040111043105710.0009288852205177990.00675099815905765
HMGN3#932458.178547723350592.73180911341838e-050.000582973870037397
MXI1#460159.96157162875931.01894348670516e-050.000266844129408225
MYC#460955.22228187160940.0002573944848850610.00276848842501657
SIN3A#2594255.408884726815140.0002159522671657270.00248390295490323
TAF1#687253.343046285745290.002394600090870310.0135579333671476
TBP#690853.706770687096390.001428755106721120.00920529022768953
TCF7L2#6934510.77017656313736.89693748574565e-060.000200252781227075
USF1#739156.361499277207969.59569864925045e-050.00137113855688749
YY1#752854.911170749853860.00034993140821360.00353242667141118



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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