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Coexpression cluster:C3487: Difference between revisions

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|ontology_enrichment_disease=DOID:162!7.97e-23!235;DOID:14566!1.28e-22!239;DOID:0050687!2.44e-14!143;DOID:305!8.62e-13!106;DOID:0050686!3.83e-12!137;DOID:7!7.08e-08!39
|ontology_enrichment_disease=DOID:162!7.97e-23!235;DOID:14566!1.28e-22!239;DOID:0050687!2.44e-14!143;DOID:305!8.62e-13!106;DOID:0050686!3.83e-12!137;DOID:7!7.08e-08!39
|ontology_enrichment_uberon=UBERON:0001869!5.83e-17!32;UBERON:0001893!5.98e-17!34;UBERON:0002791!3.15e-16!33;UBERON:0002020!9.78e-15!34;UBERON:0003528!9.78e-15!34;UBERON:0003080!1.14e-13!42;UBERON:0002780!1.56e-13!41;UBERON:0001890!1.56e-13!41;UBERON:0006240!1.56e-13!41;UBERON:0002619!2.87e-13!22;UBERON:0000955!3.09e-13!69;UBERON:0006238!3.09e-13!69;UBERON:0000956!8.05e-13!25;UBERON:0000203!8.05e-13!25;UBERON:0001950!3.65e-12!20;UBERON:0001049!2.77e-11!57;UBERON:0005068!2.77e-11!57;UBERON:0006241!2.77e-11!57;UBERON:0007135!2.77e-11!57;UBERON:0003056!3.57e-11!61;UBERON:0000481!6.60e-11!347;UBERON:0000073!2.39e-10!94;UBERON:0001016!2.39e-10!94;UBERON:0000033!2.52e-10!123;UBERON:0002616!4.55e-10!59;UBERON:0003075!8.91e-10!86;UBERON:0007284!8.91e-10!86;UBERON:0000153!1.03e-09!129;UBERON:0007811!1.03e-09!129;UBERON:0001017!1.09e-09!82;UBERON:0002346!1.14e-09!90;UBERON:0005743!2.80e-09!86;UBERON:0005409!1.79e-08!35;UBERON:0000064!8.19e-08!219;UBERON:0001007!1.06e-07!155;UBERON:0001555!1.06e-07!155;UBERON:0007026!1.06e-07!155;UBERON:0000924!1.53e-07!173;UBERON:0006601!1.53e-07!173;UBERON:0004121!1.67e-07!169;UBERON:0000475!7.10e-07!365
|ontology_enrichment_uberon=UBERON:0001869!5.83e-17!32;UBERON:0001893!5.98e-17!34;UBERON:0002791!3.15e-16!33;UBERON:0002020!9.78e-15!34;UBERON:0003528!9.78e-15!34;UBERON:0003080!1.14e-13!42;UBERON:0002780!1.56e-13!41;UBERON:0001890!1.56e-13!41;UBERON:0006240!1.56e-13!41;UBERON:0002619!2.87e-13!22;UBERON:0000955!3.09e-13!69;UBERON:0006238!3.09e-13!69;UBERON:0000956!8.05e-13!25;UBERON:0000203!8.05e-13!25;UBERON:0001950!3.65e-12!20;UBERON:0001049!2.77e-11!57;UBERON:0005068!2.77e-11!57;UBERON:0006241!2.77e-11!57;UBERON:0007135!2.77e-11!57;UBERON:0003056!3.57e-11!61;UBERON:0000481!6.60e-11!347;UBERON:0000073!2.39e-10!94;UBERON:0001016!2.39e-10!94;UBERON:0000033!2.52e-10!123;UBERON:0002616!4.55e-10!59;UBERON:0003075!8.91e-10!86;UBERON:0007284!8.91e-10!86;UBERON:0000153!1.03e-09!129;UBERON:0007811!1.03e-09!129;UBERON:0001017!1.09e-09!82;UBERON:0002346!1.14e-09!90;UBERON:0005743!2.80e-09!86;UBERON:0005409!1.79e-08!35;UBERON:0000064!8.19e-08!219;UBERON:0001007!1.06e-07!155;UBERON:0001555!1.06e-07!155;UBERON:0007026!1.06e-07!155;UBERON:0000924!1.53e-07!173;UBERON:0006601!1.53e-07!173;UBERON:0004121!1.67e-07!169;UBERON:0000475!7.10e-07!365
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.018964457106539!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0324504002306318!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00436388823237774!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.032138222643374!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319855380742108!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269168109852266!SMARCC1#6599;3:43.6633593196315:1.20046018043203e-05:0.00030130944672949!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246004908292266!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247753198367226!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00614231554583672!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0139866542015019
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31551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.00477066,1.15329e-05,0.137332,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.00340073,0.000943525,0.201033,0.0488949,0.174921,0.00132287,0.0330727,0.00956472,0.00211059,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,8.30376e-07,0.0286025,0.000180779,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.00176415,0.0027004,0.286988,0.0761239,0.172491,0.0818785,0.182701,0.00836526,0.011488,0.141463,0.167267,0.140622,0.0889592,0.00643528,0.0458479,0.0473033,0.094881,8.21254e-10,0.00924871,0.0774373,0.109194,0.128564,0.131452,0.00128046,3.14016e-06,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.047822,0.288159,0.21727,0.0465945,0.119215,0.192475,0.177967,0.00136406,0.057571,0.047591,0.0899568,0.0608699,0.175319,0.0505407,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,4.67397e-05,1.28372e-06,0.206454,0.218192,0.108277,0.0673484,0.00613985,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.00500888,0.152372,0.194941,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,4.25963e-09,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.00326415,0.288096,0.11903,0.0838874,0.0622625,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,1.5258e-05,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,9.19731e-07,0.0590944,0.247324,5.31e-05,0.0020701,0.231073,0.0972686,6.78596e-05,0.0360851,9.84014e-08,0.131093,0.0434602,0.133616,0.0177337,0.36927,0.449036,0.407369,0.231447,0.0455669,0.43956,0.0116789,0.42622,0.448797,0.197484,0.396996,0.36145,1.77931e-05,0.381071,0.580441,0.276075,0.11074,0.00207232,0.390366,0.0049331,0.153829,0.117158,0.522904,2.0991e-06,3.95207e-08,0.227104,0.518585,0.0734371,0.0867545,0.284625,9.19242e-05,0.04783,0.144318,0.000430404,0.164197,0.0252589,0.287881,0.000261949,0.0283889,0.336276,0.468444,0.258219,0.446557,0.243383,0.000933637,0.390974,0.149257,0.029557,0.161598,0.0527155,0.000709044,0.0323708,0.0239796,0.0805771,0.000199981,0.477353,9.94932e-09,0.399222,5.84732e-08,0.20342,0.200493,0.20558,0.300504,0.00348292,0.107337,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.00677445,0.354789,0.163828,0.230581,0.120226,0.28424,0.0513026,0.314429,0.181415,0.282286,0.446891,0.0727621,0.408413,0.516511,0.0073454,0.0234043,0.33942,0.243065,0.387276,0.169614,2.18573e-09,0.537348,0.222037,0.416621,0.0174635,0.462712,0.148994,0.0019893,0.204817,0.452428,0.138871,2.79004e-06,0.166905,0.0210039,0.0833851,0.056391,3.40542e-08,0.175199,0.332919,0.373557,0.00101302,0.000216517,0.365487,0.534741,5.83009e-08,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.00388821,0.305885,0.241132,0.0795725,0.30666,0.303709,0.495883,0.386538,0.508064,0.250964,0.383276,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.0254647,0.0663581,0.307334,0.459728,0.283463,0.000222968,0.472935,0.0151656,0.273281,0.368095,0.275089,0.0133102,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.00817676,0.00107377,0.299887,0.634365,0.205413,0.17639,0.0779009,0.00446098,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.0358457,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.310674,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.00145205,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.00316602,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.000191608,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.00467879,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.0120432,0.078016,0.0407233,0.0537355,0.319922,0.261724,0.00186843,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.0037817,0.255956,0.200105,0.227491,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.2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}}
}}

Revision as of 13:12, 5 September 2012


Full id: C3487_mucinous_brain_temporal_cerebral_stomach_postcentral_occipital



Phase1 CAGE Peaks

Hg19::chr15:41786021..41786055,+p2@ITPKA
Hg19::chr15:41786065..41786081,+p1@ITPKA
Hg19::chr15:41786087..41786090,+p8@ITPKA


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><br>uberon_data<br>disease_data<br>


Uber Anatomy
Ontology termp-valuen
cerebral hemisphere5.83e-1732
telencephalon5.98e-1734
regional part of telencephalon3.15e-1633
gray matter9.78e-1534
brain grey matter9.78e-1534
anterior neural tube1.14e-1342
regional part of forebrain1.56e-1341
forebrain1.56e-1341
future forebrain1.56e-1341
regional part of cerebral cortex2.87e-1322
brain3.09e-1369
future brain3.09e-1369
cerebral cortex8.05e-1325
pallium8.05e-1325
neocortex3.65e-1220
neural tube2.77e-1157
neural rod2.77e-1157
future spinal cord2.77e-1157
neural keel2.77e-1157
pre-chordal neural plate3.57e-1161
multi-tissue structure6.60e-11347
regional part of nervous system2.39e-1094
nervous system2.39e-1094
head2.52e-10123
regional part of brain4.55e-1059
neural plate8.91e-1086
presumptive neural plate8.91e-1086
anterior region of body1.03e-09129
craniocervical region1.03e-09129
central nervous system1.09e-0982
neurectoderm1.14e-0990
gastrointestinal system1.79e-0835
organ part8.19e-08219
digestive system1.06e-07155
digestive tract1.06e-07155
primitive gut1.06e-07155
ectoderm1.53e-07173
presumptive ectoderm1.53e-07173
ectoderm-derived structure1.67e-07169
organism subdivision7.10e-07365
Disease
Ontology termp-valuen
cancer7.97e-23235
disease of cellular proliferation1.28e-22239
cell type cancer2.44e-14143
carcinoma8.62e-13106
organ system cancer3.83e-12137
disease of anatomical entity7.08e-0839


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#90536.336201576962630.003930750035764890.018964457106539
E2F1#186934.907389214879320.008460985347239390.0324504002306318
E2F4#1874312.66806031528440.0004917987006298980.00436388823237774
E2F6#187635.017155731697390.00791769806886330.032138222643374
EGR1#195834.988179094810140.008056488137383440.0319855380742108
NFKB1#479035.488063424193840.006049381815655430.0269168109852266
SMARCC1#6599343.66335931963151.20046018043203e-050.00030130944672949
SP1#666735.69838137814090.005403962701712170.0246004908292266
TFAP2A#7020316.5186343730450.0002218033880766340.00247753198367226
TFAP2C#7022310.80922860986020.0007916746575753130.00614231554583672
ZBTB7A#5134137.35190930787590.002516255860282270.0139866542015019



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.