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Coexpression cluster:C2764: Difference between revisions

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|full_id=C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma
|full_id=C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma
|id=C2764
|id=C2764
|ontology_enrichment_celltype=CL:0000220!3.25e-37!246;CL:0002321!5.84e-37!248;CL:0000055!8.50e-36!180;CL:0000222!7.49e-21!119;CL:0000680!5.29e-19!57;CL:0000056!5.29e-19!57;CL:0000355!5.29e-19!57;CL:0000548!5.26e-18!679;CL:0000004!5.26e-18!679;CL:0000255!5.26e-18!679;CL:0000183!8.54e-18!59;CL:0000187!1.53e-17!54;CL:0000012!3.33e-17!682;CL:0000066!1.02e-16!254;CL:0000393!1.75e-16!60;CL:0000211!1.75e-16!60;CL:0000192!6.06e-16!42;CL:0000514!6.06e-16!42;CL:0000359!1.02e-15!32;CL:0000057!9.88e-13!75;CL:0000144!3.17e-12!625;CL:0002371!7.49e-11!591;CL:0000221!3.77e-10!71;CL:0000133!6.63e-08!59;CL:0000003!1.61e-07!722
|ontology_enrichment_celltype=CL:0002321!1.64e-36!250;CL:0000548!5.68e-23!679;CL:0000255!5.68e-23!679;CL:0000055!8.15e-22!106;CL:0000222!3.16e-21!121;CL:0000680!1.65e-19!58;CL:0000056!1.65e-19!58;CL:0000355!1.65e-19!58;CL:0000183!1.93e-18!59;CL:0000187!5.62e-18!55;CL:0000393!5.47e-17!61;CL:0000211!5.47e-17!61;CL:0000192!1.47e-16!43;CL:0000514!1.47e-16!43;CL:0000359!1.57e-16!32;CL:0002371!1.53e-15!588;CL:0000066!1.41e-14!253;CL:0000057!9.08e-14!76;CL:0000003!6.35e-12!722;CL:0000221!2.21e-10!72;CL:0000133!3.42e-08!59
|ontology_enrichment_disease=DOID:2394!4.12e-08!14;DOID:120!3.51e-07!27;DOID:193!6.16e-07!29
|ontology_enrichment_disease=DOID:2394!2.08e-08!14;DOID:120!9.87e-07!27
|ontology_enrichment_uberon=UBERON:0005256!1.04e-24!143;UBERON:0000119!2.58e-23!312;UBERON:0000475!7.95e-23!365;UBERON:0000483!1.13e-22!309;UBERON:0003914!6.91e-21!118;UBERON:0000486!1.43e-20!82;UBERON:0002100!7.30e-20!216;UBERON:0000914!3.74e-19!83;UBERON:0002329!3.74e-19!83;UBERON:0003077!3.74e-19!83;UBERON:0003059!3.74e-19!83;UBERON:0007282!3.74e-19!83;UBERON:0009618!3.74e-19!83;UBERON:0007285!3.74e-19!83;UBERON:0004290!1.81e-18!70;UBERON:0000490!1.99e-18!138;UBERON:0000481!1.79e-17!347;UBERON:0001134!5.76e-17!61;UBERON:0002036!5.76e-17!61;UBERON:0003082!5.76e-17!61;UBERON:0003104!1.25e-16!238;UBERON:0009142!1.25e-16!238;UBERON:0002049!1.84e-16!79;UBERON:0007798!1.84e-16!79;UBERON:0002385!4.40e-16!63;UBERON:0001015!4.40e-16!63;UBERON:0000383!4.40e-16!63;UBERON:0001637!1.84e-15!42;UBERON:0003509!1.84e-15!42;UBERON:0004572!1.84e-15!42;UBERON:0000468!5.22e-15!659;UBERON:0000467!7.95e-14!625;UBERON:0000480!1.45e-13!626;UBERON:0004872!3.37e-13!84;UBERON:0001981!3.96e-13!60;UBERON:0007500!3.96e-13!60;UBERON:0004537!3.96e-13!60;UBERON:0006965!3.96e-13!60;UBERON:0000055!6.27e-13!69;UBERON:0004573!1.08e-12!33;UBERON:0004571!1.08e-12!33;UBERON:0000477!3.75e-11!286;UBERON:0001048!6.79e-11!168;UBERON:0004111!1.52e-10!241;UBERON:0002050!1.67e-10!605;UBERON:0005423!1.67e-10!605;UBERON:0004535!1.69e-10!110;UBERON:0000923!1.75e-10!604;UBERON:0005291!1.75e-10!604;UBERON:0006598!1.75e-10!604;UBERON:0002532!1.75e-10!604;UBERON:0000922!1.99e-10!612;UBERON:0001009!3.58e-10!113;UBERON:0003102!6.12e-09!95;UBERON:0000025!2.06e-08!194;UBERON:0007625!1.09e-07!11;UBERON:0000466!1.20e-07!126;UBERON:0002199!1.66e-07!45;UBERON:0002416!1.66e-07!45;UBERON:0003886!3.30e-07!63;UBERON:0005085!4.40e-07!29;UBERON:0000464!6.32e-07!104
|ontology_enrichment_uberon=UBERON:0000486!4.47e-20!83;UBERON:0000119!9.22e-20!309;UBERON:0007503!1.38e-19!78;UBERON:0000483!3.42e-19!306;UBERON:0000490!3.85e-19!148;UBERON:0003914!5.13e-19!117;UBERON:0000475!7.24e-19!264;UBERON:0002329!2.31e-18!71;UBERON:0003059!2.31e-18!71;UBERON:0007282!2.31e-18!71;UBERON:0004290!2.31e-18!71;UBERON:0009618!2.31e-18!71;UBERON:0003077!1.39e-17!72;UBERON:0007285!1.39e-17!72;UBERON:0003104!1.45e-17!160;UBERON:0009142!1.45e-17!160;UBERON:0007524!1.57e-17!73;UBERON:0005256!3.36e-17!122;UBERON:0001134!6.72e-17!62;UBERON:0002036!6.72e-17!62;UBERON:0003082!6.72e-17!62;UBERON:0002049!1.11e-16!78;UBERON:0007798!1.11e-16!78;UBERON:0001637!1.64e-16!42;UBERON:0003509!1.64e-16!42;UBERON:0004572!1.64e-16!42;UBERON:0002385!3.93e-16!64;UBERON:0001015!3.93e-16!64;UBERON:0000383!3.93e-16!64;UBERON:0002100!8.22e-16!199;UBERON:0004573!2.23e-13!33;UBERON:0004571!2.23e-13!33;UBERON:0000055!5.19e-13!68;UBERON:0007500!6.00e-13!59;UBERON:0001981!6.00e-13!59;UBERON:0004537!6.00e-13!59;UBERON:0006965!6.00e-13!59;UBERON:0004872!1.50e-12!83;UBERON:0000468!1.74e-12!656;UBERON:0000467!5.71e-12!624;UBERON:0000480!1.02e-11!625;UBERON:0000481!1.08e-11!342;UBERON:0004535!3.45e-11!109;UBERON:0001009!8.30e-11!112;UBERON:0000477!9.45e-11!373;UBERON:0003102!3.45e-09!99;UBERON:0001048!8.30e-09!160;UBERON:0000922!2.43e-08!592;UBERON:0004111!2.77e-08!240;UBERON:0005423!5.46e-08!581;UBERON:0007625!8.43e-08!11;UBERON:0002199!2.15e-07!46;UBERON:0002416!2.15e-07!46;UBERON:0000947!6.35e-07!21;UBERON:0010191!6.35e-07!21
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513145047309477!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.00129245224462406!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106686716229489!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.0099846742300575!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101590186144939!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161171996836281!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00434868813829926!FOS#2353;4:8.9979553088944:0.000152514771116863:0.00195202085547476!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186445516696366!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320166043837361!MYC#4609;4:5.2222818716094:0.00134430939527274:0.0088893458865955!NFYA#4800;4:18.4255806998305:8.67100748407158e-06:0.000234974403380631!NFYB#4801;3:12.5698449401523:0.00081145639769735:0.00619229100680356!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.043515941164299!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188586411763592!RFX5#5993;4:12.0479108271951:4.74457429336527e-05:0.000827795848020006!SP1#6667;4:5.6983813781409:0.000948260606533398:0.006853185903103!SP2#6668;4:26.1535304938446:2.13562021071447e-06:7.75798397171509e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322957100063927!TAF7#6879;3:8.57480205369294:0.0025005543351524:0.0140375937545141!TBP#6908;4:3.70677068709639:0.00529637781478435:0.024478842439185!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249589380959154
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}}
}}

Revision as of 14:23, 19 October 2012


Full id: C2764_Smooth_Lens_Renal_Ciliary_Mesothelial_mucinous_glioblastoma



Phase1 CAGE Peaks

Hg19::chr3:98620486..98620493,-p4@DCBLD2
Hg19::chr3:98620500..98620547,-p1@DCBLD2
Hg19::chr3:98620631..98620663,-p13@DCBLD2
Hg19::chr3:98620849..98620854,-p32@DCBLD2


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>

Uber Anatomy
Ontology termp-valuen
multilaminar epithelium4.47e-2083
cell layer9.22e-20309
epithelial vesicle1.38e-1978
epithelium3.42e-19306
unilaminar epithelium3.85e-19148
epithelial tube5.13e-19117
organism subdivision7.24e-19264
somite2.31e-1871
presomitic mesoderm2.31e-1871
presumptive segmental plate2.31e-1871
dermomyotome2.31e-1871
trunk paraxial mesoderm2.31e-1871
paraxial mesoderm1.39e-1772
presumptive paraxial mesoderm1.39e-1772
mesenchyme1.45e-17160
entire embryonic mesenchyme1.45e-17160
dense mesenchyme tissue1.57e-1773
trunk mesenchyme3.36e-17122
skeletal muscle tissue6.72e-1762
striated muscle tissue6.72e-1762
myotome6.72e-1762
vasculature1.11e-1678
vascular system1.11e-1678
artery1.64e-1642
arterial blood vessel1.64e-1642
arterial system1.64e-1642
muscle tissue3.93e-1664
musculature3.93e-1664
musculature of body3.93e-1664
trunk8.22e-16199
systemic artery2.23e-1333
systemic arterial system2.23e-1333
vessel5.19e-1368
epithelial tube open at both ends6.00e-1359
blood vessel6.00e-1359
blood vasculature6.00e-1359
vascular cord6.00e-1359
splanchnic layer of lateral plate mesoderm1.50e-1283
multi-cellular organism1.74e-12656
anatomical system5.71e-12624
anatomical group1.02e-11625
multi-tissue structure1.08e-11342
cardiovascular system3.45e-11109
circulatory system8.30e-11112
anatomical cluster9.45e-11373
surface structure3.45e-0999
primordium8.30e-09160
embryo2.43e-08592
anatomical conduit2.77e-08240
developing anatomical structure5.46e-08581
pigment epithelium of eye8.43e-0811
integument2.15e-0746
integumental system2.15e-0746
aorta6.35e-0721
aortic system6.35e-0721
Disease
Ontology termp-valuen
ovarian cancer2.08e-0814
female reproductive organ cancer9.87e-0727


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#90546.336201576962630.0006203100587215640.00513145047309477
CHD2#1106410.34402283411698.73193255208051e-050.00129245224462406
E2F1#186944.907389214879320.001724022357361790.0106686716229489
E2F6#187645.017155731697390.00157802193473060.0099846742300575
EGR1#195844.988179094810140.001615011500076050.0101590186144939
ELF1#199744.258097958807540.003041525565781240.0161171996836281
EP300#203346.77394172622320.0004748459821442640.00434868813829926
FOS#235348.99795530889440.0001525147711168630.00195202085547476
HEY1#2346244.040111043105710.00375304636917980.0186445516696366
IRF1#365935.727872815172930.008097114790333330.0320166043837361
MYC#460945.22228187160940.001344309395272740.0088893458865955
NFYA#4800418.42558069983058.67100748407158e-060.000234974403380631
NFYB#4801312.56984494015230.000811456397697350.00619229100680356
PAX5#507935.002174148383370.01196533174786410.043515941164299
POU2F2#545249.106124057742520.000145395665174930.00188586411763592
RFX5#5993412.04791082719514.74457429336527e-050.000827795848020006
SP1#666745.69838137814090.0009482606065333980.006853185903103
SP2#6668426.15353049384462.13562021071447e-067.75798397171509e-05
TAF1#687243.343046285745290.008005664898701650.0322957100063927
TAF7#687938.574802053692940.00250055433515240.0140375937545141
TBP#690843.706770687096390.005296377814784350.024478842439185
ZNF263#1012748.221841637010680.0002187871180958320.00249589380959154



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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