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Coexpression cluster:C3864: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.49e-22!106;DOID:0050687!2.83e-19!143;DOID:162!1.25e-10!235;DOID:14566!2.41e-10!239;DOID:299!4.83e-10!25
|ontology_enrichment_disease=DOID:305!4.49e-22!106;DOID:0050687!2.83e-19!143;DOID:162!1.25e-10!235;DOID:14566!2.41e-10!239;DOID:299!4.83e-10!25
|ontology_enrichment_uberon=UBERON:0004119!4.60e-17!169;UBERON:0000925!4.60e-17!169;UBERON:0006595!4.60e-17!169;UBERON:0007023!8.00e-16!115;UBERON:0004921!4.25e-15!129;UBERON:0004185!4.25e-15!129;UBERON:0001007!9.97e-15!155;UBERON:0001555!9.97e-15!155;UBERON:0007026!9.97e-15!155;UBERON:0005177!1.09e-13!107;UBERON:0000077!1.82e-13!130;UBERON:0000064!5.06e-13!219;UBERON:0000466!1.19e-12!126;UBERON:0005911!6.61e-12!82;UBERON:0000062!1.01e-11!511;UBERON:0001049!1.03e-11!57;UBERON:0005068!1.03e-11!57;UBERON:0006241!1.03e-11!57;UBERON:0007135!1.03e-11!57;UBERON:0000464!1.12e-10!104;UBERON:0004121!1.17e-10!169;UBERON:0003075!1.39e-10!86;UBERON:0007284!1.39e-10!86;UBERON:0001041!1.57e-10!98;UBERON:0005743!5.34e-10!86;UBERON:0000924!5.81e-10!173;UBERON:0006601!5.81e-10!173;UBERON:0000073!7.58e-10!94;UBERON:0001016!7.58e-10!94;UBERON:0002346!1.54e-09!90;UBERON:0001017!3.02e-09!82;UBERON:0000481!3.77e-09!347;UBERON:0002616!9.74e-09!59;UBERON:0000153!1.03e-08!129;UBERON:0007811!1.03e-08!129;UBERON:0003080!2.09e-08!42;UBERON:0003056!2.21e-08!61;UBERON:0000033!2.33e-08!123;UBERON:0009569!2.51e-08!113;UBERON:0000955!2.68e-08!69;UBERON:0006238!2.68e-08!69;UBERON:0002780!3.28e-08!41;UBERON:0001890!3.28e-08!41;UBERON:0006240!3.28e-08!41;UBERON:0005172!9.67e-08!55;UBERON:0005173!9.67e-08!55;UBERON:0002020!1.54e-07!34;UBERON:0003528!1.54e-07!34;UBERON:0000922!1.73e-07!612;UBERON:0004111!1.95e-07!241;UBERON:0001893!2.04e-07!34;UBERON:0002791!3.01e-07!33;UBERON:0002048!5.07e-07!22;UBERON:0000117!5.07e-07!22;UBERON:0000171!5.07e-07!22;UBERON:0000170!5.07e-07!22;UBERON:0005597!5.07e-07!22;UBERON:0000118!5.07e-07!22;UBERON:0005409!6.96e-07!35;UBERON:0001004!8.40e-07!72;UBERON:0001008!9.13e-07!45;UBERON:0000063!9.26e-07!97
|ontology_enrichment_uberon=UBERON:0004119!4.60e-17!169;UBERON:0000925!4.60e-17!169;UBERON:0006595!4.60e-17!169;UBERON:0007023!8.00e-16!115;UBERON:0004921!4.25e-15!129;UBERON:0004185!4.25e-15!129;UBERON:0001007!9.97e-15!155;UBERON:0001555!9.97e-15!155;UBERON:0007026!9.97e-15!155;UBERON:0005177!1.09e-13!107;UBERON:0000077!1.82e-13!130;UBERON:0000064!5.06e-13!219;UBERON:0000466!1.19e-12!126;UBERON:0005911!6.61e-12!82;UBERON:0000062!1.01e-11!511;UBERON:0001049!1.03e-11!57;UBERON:0005068!1.03e-11!57;UBERON:0006241!1.03e-11!57;UBERON:0007135!1.03e-11!57;UBERON:0000464!1.12e-10!104;UBERON:0004121!1.17e-10!169;UBERON:0003075!1.39e-10!86;UBERON:0007284!1.39e-10!86;UBERON:0001041!1.57e-10!98;UBERON:0005743!5.34e-10!86;UBERON:0000924!5.81e-10!173;UBERON:0006601!5.81e-10!173;UBERON:0000073!7.58e-10!94;UBERON:0001016!7.58e-10!94;UBERON:0002346!1.54e-09!90;UBERON:0001017!3.02e-09!82;UBERON:0000481!3.77e-09!347;UBERON:0002616!9.74e-09!59;UBERON:0000153!1.03e-08!129;UBERON:0007811!1.03e-08!129;UBERON:0003080!2.09e-08!42;UBERON:0003056!2.21e-08!61;UBERON:0000033!2.33e-08!123;UBERON:0009569!2.51e-08!113;UBERON:0000955!2.68e-08!69;UBERON:0006238!2.68e-08!69;UBERON:0002780!3.28e-08!41;UBERON:0001890!3.28e-08!41;UBERON:0006240!3.28e-08!41;UBERON:0005172!9.67e-08!55;UBERON:0005173!9.67e-08!55;UBERON:0002020!1.54e-07!34;UBERON:0003528!1.54e-07!34;UBERON:0000922!1.73e-07!612;UBERON:0004111!1.95e-07!241;UBERON:0001893!2.04e-07!34;UBERON:0002791!3.01e-07!33;UBERON:0002048!5.07e-07!22;UBERON:0000117!5.07e-07!22;UBERON:0000171!5.07e-07!22;UBERON:0000170!5.07e-07!22;UBERON:0005597!5.07e-07!22;UBERON:0000118!5.07e-07!22;UBERON:0005409!6.96e-07!35;UBERON:0001004!8.40e-07!72;UBERON:0001008!9.13e-07!45;UBERON:0000063!9.26e-07!97
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475,0.0558058,0.28262,0.517717,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,8.47333e-05,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.00896808,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,0.0774373,0.109194,0.128564,0.131452,0.112518,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.00264443,0.0232393,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,2.90292e-07,0.000581378,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.194941,0.000125914,0.101607,0.00771936,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.15663,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.00102368,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.257598,0.103667,0.113069,0.025556,0.16791,0.09066,0.0597157,0.000886556,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.407281,0.000500398,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.36927,0.449036,0.407369,0.231447,0.544776,0.43956,0.37006,0.42622,0.448797,0.197484,0.396996,0.0107863,0.00202987,0.381071,0.057779,0.643768,0.432035,0.0411943,0.390366,0.0305485,0.50058,0.443185,0.522904,0.000322406,0.00516504,0.227104,0.518585,0.617852,0.38649,0.284625,0.0344717,0.192225,0.729153,0.28907,0.164197,0.462688,0.287881,0.0556235,0.478174,0.336276,0.468444,0.00355636,0.446557,0.243383,0.000171205,0.390974,0.73485,0.319063,0.161598,0.405056,0.00422412,0.150692,0.00613559,0.37357,5.07251e-06,0.477353,6.7495e-07,0.399222,3.61308e-06,1.5821e-07,0.200493,0.20558,0.300504,0.25656,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.562405,0.314429,0.181415,0.282286,0.000976922,0.0165273,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,1.90459e-08,0.180745,0.222037,0.416621,0.416292,0.462712,0.734551,0.579431,0.204817,0.452428,0.138871,0.308032,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.0768488,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.00438156,0.0830022,0.305885,0.241132,0.371414,0.0527347,0.303709,0.0323359,0.386538,0.00602464,0.250964,0.383276,0.457886,0.504711,0.220231,0.159791,0.196976,0.191517,0.129584,0.0145214,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.0153645,0.387069,0.332774,0.52832,0.299887,0.266492,0.205413,0.17639,8.36739e-05,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.00386277,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.00111175,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.0315594,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.280943,0.0257454,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.211332,0.187731,0.233626,0.00132285,0.0812887,0.0981146,0.064145,0.121913,4.56072e-05,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.00335066,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.00144649,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604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}}
}}

Revision as of 11:50, 5 September 2012


Full id: C3864_small_Intestinal_serous_choriocarcinoma_Hepatocyte_rectal_Prostate



Phase1 CAGE Peaks

Hg19::chr1:151483855..151483871,+p2@CGN
Hg19::chr1:151483881..151483912,+p1@CGN
Hg19::chr1:151483924..151483940,+p3@CGN


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 cell1.23e-18254
endodermal cell2.09e-1159
endo-epithelial cell9.51e-1043
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.60e-17169
endoderm4.60e-17169
presumptive endoderm4.60e-17169
adult organism8.00e-16115
subdivision of digestive tract4.25e-15129
endodermal part of digestive tract4.25e-15129
digestive system9.97e-15155
digestive tract9.97e-15155
primitive gut9.97e-15155
trunk region element1.09e-13107
mixed endoderm/mesoderm-derived structure1.82e-13130
organ part5.06e-13219
immaterial anatomical entity1.19e-12126
endo-epithelium6.61e-1282
organ1.01e-11511
neural tube1.03e-1157
neural rod1.03e-1157
future spinal cord1.03e-1157
neural keel1.03e-1157
anatomical space1.12e-10104
ectoderm-derived structure1.17e-10169
neural plate1.39e-1086
presumptive neural plate1.39e-1086
foregut1.57e-1098
ectoderm5.81e-10173
presumptive ectoderm5.81e-10173
regional part of nervous system7.58e-1094
nervous system7.58e-1094
neurectoderm1.54e-0990
central nervous system3.02e-0982
multi-tissue structure3.77e-09347
regional part of brain9.74e-0959
anterior region of body1.03e-08129
craniocervical region1.03e-08129
anterior neural tube2.09e-0842
pre-chordal neural plate2.21e-0861
head2.33e-08123
subdivision of trunk2.51e-08113
brain2.68e-0869
future brain2.68e-0869
regional part of forebrain3.28e-0841
forebrain3.28e-0841
future forebrain3.28e-0841
abdomen element9.67e-0855
abdominal segment element9.67e-0855
gray matter1.54e-0734
brain grey matter1.54e-0734
embryo1.73e-07612
anatomical conduit1.95e-07241
telencephalon2.04e-0734
regional part of telencephalon3.01e-0733
lung5.07e-0722
respiratory tube5.07e-0722
respiration organ5.07e-0722
pair of lungs5.07e-0722
lung primordium5.07e-0722
lung bud5.07e-0722
gastrointestinal system6.96e-0735
respiratory system8.40e-0772
renal system9.13e-0745
organ segment9.26e-0797
Disease
Ontology termp-valuen
carcinoma4.49e-22106
cell type cancer2.83e-19143
cancer1.25e-10235
disease of cellular proliferation2.41e-10239
adenocarcinoma4.83e-1025


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
E2F1#186934.907389214879320.008460985347239390.0325436175995409
E2F6#187635.017155731697390.00791769806886330.0322296631957756
EGR1#195834.988179094810140.008056488137383440.0320708783572263
MAX#414936.452555509007120.003721913834265510.0186558340822065
MYC#460935.22228187160940.007020843755740150.0294560680113183
PAX5#507936.669565531177830.003370290999677260.0172950973720172
USF1#739136.361499277207960.00388404057290560.0190309788127463
USF2#7392312.99219738506960.0004558979393427810.00421657145651973
YY1#752834.911170749853860.008441455341808260.0329477970865951
ZBTB7A#5134137.35190930787590.002516255860282270.0140232254958388



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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