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Coexpression cluster:C3299: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.30e-18!106;DOID:0050687!3.50e-14!143;DOID:299!2.23e-08!25
|ontology_enrichment_disease=DOID:305!1.30e-18!106;DOID:0050687!3.50e-14!143;DOID:299!2.23e-08!25
|ontology_enrichment_uberon=UBERON:0007023!1.16e-27!115;UBERON:0004119!3.58e-18!169;UBERON:0000925!3.58e-18!169;UBERON:0006595!3.58e-18!169;UBERON:0001049!5.36e-16!57;UBERON:0005068!5.36e-16!57;UBERON:0006241!5.36e-16!57;UBERON:0007135!5.36e-16!57;UBERON:0001007!1.14e-15!155;UBERON:0001555!1.14e-15!155;UBERON:0007026!1.14e-15!155;UBERON:0000062!2.62e-15!511;UBERON:0004921!4.80e-15!129;UBERON:0004185!4.80e-15!129;UBERON:0000481!1.78e-14!347;UBERON:0000064!5.48e-14!219;UBERON:0000475!1.60e-13!365;UBERON:0000077!2.76e-13!130;UBERON:0002616!5.11e-13!59;UBERON:0003080!1.83e-12!42;UBERON:0001017!2.45e-12!82;UBERON:0002780!3.74e-12!41;UBERON:0001890!3.74e-12!41;UBERON:0006240!3.74e-12!41;UBERON:0005743!4.84e-12!86;UBERON:0000955!1.50e-11!69;UBERON:0006238!1.50e-11!69;UBERON:0004121!2.02e-11!169;UBERON:0000466!3.25e-11!126;UBERON:0000153!1.63e-10!129;UBERON:0007811!1.63e-10!129;UBERON:0000924!2.09e-10!173;UBERON:0006601!2.09e-10!173;UBERON:0001893!2.10e-10!34;UBERON:0002020!2.56e-10!34;UBERON:0003528!2.56e-10!34;UBERON:0000073!4.45e-10!94;UBERON:0001016!4.45e-10!94;UBERON:0001041!4.63e-10!98;UBERON:0000033!5.17e-10!123;UBERON:0002791!5.55e-10!33;UBERON:0003075!7.22e-10!86;UBERON:0007284!7.22e-10!86;UBERON:0005911!1.21e-09!82;UBERON:0001869!2.98e-09!32;UBERON:0000468!6.86e-09!659;UBERON:0000483!7.05e-09!309;UBERON:0005177!8.22e-09!107;UBERON:0002619!9.55e-09!22;UBERON:0000119!1.40e-08!312;UBERON:0002346!1.53e-08!90;UBERON:0000922!2.07e-08!612;UBERON:0004111!2.60e-08!241;UBERON:0000464!4.62e-08!104;UBERON:0001950!5.29e-08!20;UBERON:0000477!2.01e-07!286;UBERON:0001004!2.07e-07!72;UBERON:0003056!3.53e-07!61;UBERON:0000480!3.74e-07!626;UBERON:0000467!4.34e-07!625;UBERON:0002050!5.56e-07!605;UBERON:0005423!5.56e-07!605;UBERON:0000923!8.51e-07!604;UBERON:0005291!8.51e-07!604;UBERON:0006598!8.51e-07!604;UBERON:0002532!8.51e-07!604
|ontology_enrichment_uberon=UBERON:0007023!1.16e-27!115;UBERON:0004119!3.58e-18!169;UBERON:0000925!3.58e-18!169;UBERON:0006595!3.58e-18!169;UBERON:0001049!5.36e-16!57;UBERON:0005068!5.36e-16!57;UBERON:0006241!5.36e-16!57;UBERON:0007135!5.36e-16!57;UBERON:0001007!1.14e-15!155;UBERON:0001555!1.14e-15!155;UBERON:0007026!1.14e-15!155;UBERON:0000062!2.62e-15!511;UBERON:0004921!4.80e-15!129;UBERON:0004185!4.80e-15!129;UBERON:0000481!1.78e-14!347;UBERON:0000064!5.48e-14!219;UBERON:0000475!1.60e-13!365;UBERON:0000077!2.76e-13!130;UBERON:0002616!5.11e-13!59;UBERON:0003080!1.83e-12!42;UBERON:0001017!2.45e-12!82;UBERON:0002780!3.74e-12!41;UBERON:0001890!3.74e-12!41;UBERON:0006240!3.74e-12!41;UBERON:0005743!4.84e-12!86;UBERON:0000955!1.50e-11!69;UBERON:0006238!1.50e-11!69;UBERON:0004121!2.02e-11!169;UBERON:0000466!3.25e-11!126;UBERON:0000153!1.63e-10!129;UBERON:0007811!1.63e-10!129;UBERON:0000924!2.09e-10!173;UBERON:0006601!2.09e-10!173;UBERON:0001893!2.10e-10!34;UBERON:0002020!2.56e-10!34;UBERON:0003528!2.56e-10!34;UBERON:0000073!4.45e-10!94;UBERON:0001016!4.45e-10!94;UBERON:0001041!4.63e-10!98;UBERON:0000033!5.17e-10!123;UBERON:0002791!5.55e-10!33;UBERON:0003075!7.22e-10!86;UBERON:0007284!7.22e-10!86;UBERON:0005911!1.21e-09!82;UBERON:0001869!2.98e-09!32;UBERON:0000468!6.86e-09!659;UBERON:0000483!7.05e-09!309;UBERON:0005177!8.22e-09!107;UBERON:0002619!9.55e-09!22;UBERON:0000119!1.40e-08!312;UBERON:0002346!1.53e-08!90;UBERON:0000922!2.07e-08!612;UBERON:0004111!2.60e-08!241;UBERON:0000464!4.62e-08!104;UBERON:0001950!5.29e-08!20;UBERON:0000477!2.01e-07!286;UBERON:0001004!2.07e-07!72;UBERON:0003056!3.53e-07!61;UBERON:0000480!3.74e-07!626;UBERON:0000467!4.34e-07!625;UBERON:0002050!5.56e-07!605;UBERON:0005423!5.56e-07!605;UBERON:0000923!8.51e-07!604;UBERON:0005291!8.51e-07!604;UBERON:0006598!8.51e-07!604;UBERON:0002532!8.51e-07!604
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97897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.0443426,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.00294748,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.0117175,0.0330727,0.00100273,0.219556,0.0394698,0.0596469,0.103658,0.122476,0.108872,0.11002,0.0376172,0.0286025,0.0470027,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.000434303,0.0774373,0.00619136,0.128564,0.131452,0.323837,0.0226843,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.389379,0.0926491,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.00583965,0.0713214,0.223874,0.0472142,0.0355833,0.125606,0.175094,0.000919297,0.145116,0.206454,0.218192,0.000230242,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.0277579,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.00207136,0.101607,0.060512,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.0282663,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.0147868,0.188651,0.0813902,0.184948,0.156261,0.311847,0.0362615,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0972686,0.252227,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.103051,0.36927,0.449036,0.407369,0.231447,0.544776,0.115047,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.0966095,0.381071,0.057779,0.643768,0.432035,0.00207232,0.390366,0.48809,0.50058,0.117158,0.522904,0.00567172,0.151996,0.227104,0.518585,0.617852,0.38649,0.284625,0.156746,0.192225,0.0437169,0.0465139,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.00448654,0.390974,0.0115792,0.00120937,0.161598,0.0527155,0.00422412,0.496032,0.0239796,0.37357,0.0203982,0.477353,0.069689,0.0508568,0.00415823,0.20342,0.200493,0.20558,0.300504,0.25656,0.0189087,0.349197,0.383291,0.156104,0.141318,0.00217346,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.000976922,0.24884,0.408413,0.0374737,0.322213,0.656109,0.33942,0.0156581,0.387276,0.0391112,0.802166,0.537348,0.222037,0.416621,0.416292,0.462712,0.00246111,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.0210039,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.0393909,0.408861,0.0768488,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.00141394,0.4466,0.351067,0.275347,0.019895,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.00602464,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.463751,0.0663581,0.307334,0.459728,0.283463,0.0517073,0.0272975,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0690807,0.0870376,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.0828367,0.255516,0.20753,0.119514,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.00178902,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.0273485,0.246105,0.173026,0.200432,0.139785,0.0208458,0.240478,0.0129343,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.00553696,0.0457063,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.0445413,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0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}}
}}

Revision as of 13:40, 5 September 2012


Full id: C3299_serous_signet_skeletal_optic_colon_breast_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr12:56473883..56473903,+p2@ERBB3
Hg19::chr12:56473910..56473921,+p4@ERBB3
Hg19::chr12:56473939..56473994,+p1@ERBB3


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 cell4.14e-17254
endodermal cell1.32e-0959
Uber Anatomy
Ontology termp-valuen
adult organism1.16e-27115
endoderm-derived structure3.58e-18169
endoderm3.58e-18169
presumptive endoderm3.58e-18169
neural tube5.36e-1657
neural rod5.36e-1657
future spinal cord5.36e-1657
neural keel5.36e-1657
digestive system1.14e-15155
digestive tract1.14e-15155
primitive gut1.14e-15155
organ2.62e-15511
subdivision of digestive tract4.80e-15129
endodermal part of digestive tract4.80e-15129
multi-tissue structure1.78e-14347
organ part5.48e-14219
organism subdivision1.60e-13365
mixed endoderm/mesoderm-derived structure2.76e-13130
regional part of brain5.11e-1359
anterior neural tube1.83e-1242
central nervous system2.45e-1282
regional part of forebrain3.74e-1241
forebrain3.74e-1241
future forebrain3.74e-1241
brain1.50e-1169
future brain1.50e-1169
ectoderm-derived structure2.02e-11169
immaterial anatomical entity3.25e-11126
anterior region of body1.63e-10129
craniocervical region1.63e-10129
ectoderm2.09e-10173
presumptive ectoderm2.09e-10173
telencephalon2.10e-1034
gray matter2.56e-1034
brain grey matter2.56e-1034
regional part of nervous system4.45e-1094
nervous system4.45e-1094
foregut4.63e-1098
head5.17e-10123
regional part of telencephalon5.55e-1033
neural plate7.22e-1086
presumptive neural plate7.22e-1086
endo-epithelium1.21e-0982
cerebral hemisphere2.98e-0932
multi-cellular organism6.86e-09659
epithelium7.05e-09309
trunk region element8.22e-09107
regional part of cerebral cortex9.55e-0922
cell layer1.40e-08312
neurectoderm1.53e-0890
embryo2.07e-08612
anatomical conduit2.60e-08241
anatomical space4.62e-08104
neocortex5.29e-0820
anatomical cluster2.01e-07286
respiratory system2.07e-0772
pre-chordal neural plate3.53e-0761
anatomical group3.74e-07626
anatomical system4.34e-07625
embryonic structure5.56e-07605
developing anatomical structure5.56e-07605
germ layer8.51e-07604
embryonic tissue8.51e-07604
presumptive structure8.51e-07604
epiblast (generic)8.51e-07604
Disease
Ontology termp-valuen
carcinoma1.30e-18106
cell type cancer3.50e-14143
adenocarcinoma2.23e-0825


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#90536.336201576962630.003930750035764890.0189460773022544
CEBPB#105137.971147625824820.001974187055288560.0115018476998372
CHD2#1106310.34402283411690.0009033701102746880.00659032348050979
CTCF#1066435.360256373075030.0064925092527670.027868610983919
E2F6#187635.017155731697390.00791769806886330.0320945650539109
EGR1#195834.988179094810140.008056488137383440.0319478894551463
FOS#235338.99795530889440.001372499272417130.00895442600649504
FOSL1#8061339.7135797163731.59554825631833e-050.000370470129705714
FOSL2#2355316.93020060456170.0002060162053171620.00242517205445436
FOXA1#3169311.08141974938550.000734755275698670.00579979640531277
HDAC2#3066313.41562023662630.0004140761399857210.0039023369413435
HMGN3#932438.178547723350590.001827766942164210.0108441829047713
JUN#3725312.51282919233630.0005103313992726250.00443378263111502
JUNB#3726330.61063265982113.4847716247536e-050.000679764780944418
JUND#372736.994663941871030.002921845042734990.0156321179457097
MYC#460935.22228187160940.007020843755740150.0293534788232885
SIN3A#2594235.408884726815140.006318961977991520.0275747323787012
SMARCB1#6598318.25271578115740.000164397760679890.00202686078711451
SMARCC1#6599343.66335931963151.20046018043203e-050.000301164690809851
SP1#666735.69838137814090.005403962701712170.0245705032914287
TAF7#6879311.43306940492390.0006690181981945830.00541304552225318
ZBTB7A#5134137.35190930787590.002516255860282270.0139762402697452
ZNF263#1012738.221841637010680.001799043925565870.0109048374081355



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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