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Coexpression cluster:C4668: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.08e-33!115;UBERON:0005743!4.51e-26!86;UBERON:0002346!6.97e-26!90;UBERON:0003075!8.38e-26!86;UBERON:0007284!8.38e-26!86;UBERON:0000073!2.67e-25!94;UBERON:0001016!2.67e-25!94;UBERON:0001049!1.01e-24!57;UBERON:0005068!1.01e-24!57;UBERON:0006241!1.01e-24!57;UBERON:0007135!1.01e-24!57;UBERON:0001017!4.34e-23!82;UBERON:0000153!7.55e-23!129;UBERON:0007811!7.55e-23!129;UBERON:0000033!1.58e-22!123;UBERON:0002616!3.35e-22!59;UBERON:0000924!2.68e-21!173;UBERON:0006601!2.68e-21!173;UBERON:0004121!6.27e-21!169;UBERON:0000955!2.28e-20!69;UBERON:0006238!2.28e-20!69;UBERON:0003056!1.68e-19!61;UBERON:0003080!3.97e-19!42;UBERON:0000956!1.35e-18!25;UBERON:0000203!1.35e-18!25;UBERON:0002780!1.35e-18!41;UBERON:0001890!1.35e-18!41;UBERON:0006240!1.35e-18!41;UBERON:0001893!2.50e-18!34;UBERON:0002619!6.49e-18!22;UBERON:0002020!6.54e-18!34;UBERON:0003528!6.54e-18!34;UBERON:0002791!1.24e-17!33;UBERON:0001869!3.22e-17!32;UBERON:0000481!4.77e-17!347;UBERON:0001950!9.15e-17!20;UBERON:0000475!1.11e-10!365;UBERON:0000062!1.64e-10!511;UBERON:0000064!1.94e-10!219;UBERON:0000922!9.48e-10!612;UBERON:0000483!6.80e-09!309;UBERON:0000119!9.54e-09!312;UBERON:0000468!1.45e-08!659;UBERON:0002050!8.37e-08!605;UBERON:0005423!8.37e-08!605;UBERON:0005409!1.68e-07!35;UBERON:0000923!1.87e-07!604;UBERON:0005291!1.87e-07!604;UBERON:0006598!1.87e-07!604;UBERON:0002532!1.87e-07!604;UBERON:0004111!2.46e-07!241;UBERON:0000477!2.95e-07!286;UBERON:0001871!2.96e-07!7;UBERON:0000467!5.19e-07!625;UBERON:0000480!6.50e-07!626;UBERON:0003076!8.20e-07!15;UBERON:0003057!8.20e-07!15
|ontology_enrichment_uberon=UBERON:0007023!1.08e-33!115;UBERON:0005743!4.51e-26!86;UBERON:0002346!6.97e-26!90;UBERON:0003075!8.38e-26!86;UBERON:0007284!8.38e-26!86;UBERON:0000073!2.67e-25!94;UBERON:0001016!2.67e-25!94;UBERON:0001049!1.01e-24!57;UBERON:0005068!1.01e-24!57;UBERON:0006241!1.01e-24!57;UBERON:0007135!1.01e-24!57;UBERON:0001017!4.34e-23!82;UBERON:0000153!7.55e-23!129;UBERON:0007811!7.55e-23!129;UBERON:0000033!1.58e-22!123;UBERON:0002616!3.35e-22!59;UBERON:0000924!2.68e-21!173;UBERON:0006601!2.68e-21!173;UBERON:0004121!6.27e-21!169;UBERON:0000955!2.28e-20!69;UBERON:0006238!2.28e-20!69;UBERON:0003056!1.68e-19!61;UBERON:0003080!3.97e-19!42;UBERON:0000956!1.35e-18!25;UBERON:0000203!1.35e-18!25;UBERON:0002780!1.35e-18!41;UBERON:0001890!1.35e-18!41;UBERON:0006240!1.35e-18!41;UBERON:0001893!2.50e-18!34;UBERON:0002619!6.49e-18!22;UBERON:0002020!6.54e-18!34;UBERON:0003528!6.54e-18!34;UBERON:0002791!1.24e-17!33;UBERON:0001869!3.22e-17!32;UBERON:0000481!4.77e-17!347;UBERON:0001950!9.15e-17!20;UBERON:0000475!1.11e-10!365;UBERON:0000062!1.64e-10!511;UBERON:0000064!1.94e-10!219;UBERON:0000922!9.48e-10!612;UBERON:0000483!6.80e-09!309;UBERON:0000119!9.54e-09!312;UBERON:0000468!1.45e-08!659;UBERON:0002050!8.37e-08!605;UBERON:0005423!8.37e-08!605;UBERON:0005409!1.68e-07!35;UBERON:0000923!1.87e-07!604;UBERON:0005291!1.87e-07!604;UBERON:0006598!1.87e-07!604;UBERON:0002532!1.87e-07!604;UBERON:0004111!2.46e-07!241;UBERON:0000477!2.95e-07!286;UBERON:0001871!2.96e-07!7;UBERON:0000467!5.19e-07!625;UBERON:0000480!6.50e-07!626;UBERON:0003076!8.20e-07!15;UBERON:0003057!8.20e-07!15
|tf_chipseq_enrich=GTF2B#2959;3:31.9438299343242:3.06634405746243e-05:0.000629661633931024
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52322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,2.78926e-05,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.28262,0.517717,0.000481141,0.0145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.013859,7.46073e-05,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,1.30821e-10,0.0488949,0.174921,0.370421,0.0330727,0.00956472,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.00615421,0.000241884,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0015426,0.0109154,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.00501606,7.79674e-05,0.172491,0.0818785,0.182701,0.335058,0.147698,0.0105143,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.022113,0.132886,8.21586e-05,0.000236316,0.128564,0.131452,0.687347,0.0226843,0.051838,0.000176849,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.000356768,0.389379,0.0926491,0.21727,0.289306,0.119215,0.192475,0.00108376,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.00525614,0.0355833,0.125606,0.175094,0.0370461,0.936279,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.00171529,7.62774e-05,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,8.19108e-06,0.000143882,0.172425,0.00571044,0.000134535,0.057168,0.234298,0.00296278,0.286863,0.152372,0.194941,0.218271,0.101607,0.327067,0.172982,3.02049e-07,0.151597,0.0626744,0.191335,0.148574,0.504592,0.155821,6.54495e-05,0.000138924,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.0461822,0.11903,0.0838874,0.0622625,0.113145,0.112651,2.64043e-06,0.01625,0.0948451,0.0384217,0.249049,0.140533,0.00515192,0.0364628,0.103667,0.113069,0.025556,0.16791,0.00423976,0.0125264,0.166967,0.0190329,0.0813902,0.184948,0.0128995,0.311847,0.0362615,3.5988e-05,0.247324,0.178389,0.218229,0.231073,0.407281,0.0743925,0.0360851,0.412187,0.131093,0.0434602,0.00935312,0.418146,0.0115948,0.449036,0.0973145,0.0291288,0.544776,0.115047,0.37006,0.0189483,0.00038176,0.197484,0.396996,0.00010434,0.406019,0.381071,0.580441,0.643768,0.0198622,0.0411943,0.390366,0.48809,0.50058,0.443185,0.169835,0.875915,0.60734,0.227104,0.518585,0.0167433,0.00161115,0.0450114,0.504757,0.000187838,0.0108655,0.0465139,0.164197,0.462688,0.287881,0.21103,0.478174,0.00846715,0.0263888,0.0366482,0.446557,0.032364,0.000933637,0.390974,0.0458848,0.319063,0.161598,0.00310283,0.000709044,0.150692,0.00136122,0.37357,0.00106614,0.477353,0.069689,0.0508568,0.185744,0.20342,0.00158025,0.20558,0.0505073,0.25656,0.00254768,0.349197,0.383291,0.156104,0.141318,0.411941,0.0961477,0.000626916,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.0175523,0.00475227,0.194707,0.0727621,0.00208694,0.516511,0.0073454,0.656109,2.91166e-07,0.243065,0.387276,0.0391112,0.221908,0.0433137,0.222037,0.416621,0.416292,0.462712,0.734551,0.057399,0.204817,0.0233392,0.138871,0.308032,0.166905,0.00151457,0.0833851,0.000645205,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.236011,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.637444,0.305885,0.241132,0.0795725,0.30666,0.303709,7.72977e-06,0.386538,0.508064,0.250964,0.0131557,0.125961,0.504711,0.00213139,0.509064,0.196976,0.00136659,0.463751,0.235208,0.307334,0.0246928,0.0048173,0.0102434,5.55277e-05,0.0151656,0.00427533,0.0114705,0.00436817,0.0133102,0.47795,0.359231,4.98512e-06,0.197805,0.608187,0.387069,6.46213e-05,0.52832,0.299887,0.000613177,0.205413,5.06195e-05,0.0779009,0.276869,0.022685,0.0337138,0.18966,0.00358475,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,3.92648e-05,0.252184,0.378361,7.12232e-07,0.20753,0.0224033,0.179412,0.193601,0.0264253,0.222977,0.341681,0.000593893,0.0257082,0.198614,0.186804,0.123324,0.0213665,0.0325925,0.0933115,0.12405,0.00112112,0.226869,0.27872,0.0855609,0.131118,0.00178627,0.0335483,0.222339,5.35812e-05,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.000120193,0.158479,6.46971e-06,0.00145205,0.124213,0.259632,0.0532009,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,6.2467e-05,6.66781e-05,0.258496,0.00371613,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.0331281,0.0159159,0.00157872,0.139785,0.00149718,0.240478,0.156465,0.13108,0.256963,0.222798,0.0157468,0.176789,0.0969345,0.00162178,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,8.58721e-07,0.078016,0.0407233,0.0537355,0.319922,0.00371523,0.211332,0.187731,0.233626,0.189559,0.0812887,0.00497886,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,5.26612e-05,0.089609,0.0367455,0.13497,0.204393,0.295769,0.00499908,0.347036,0.141729,0.000284196,0.0359756,0.200105,0.00236454,0.00569858,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.0213159,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.00135479,0.281727,0.283218,0.0342254,0.164638,0.224257,0.0935776,1.07484e-08,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.00414049,0.101021,0.000136918,1.92492e-06,0.157274,0.0251447,0.252796,0.205954,0.000104314
}}
}}

Revision as of 14:13, 5 September 2012


Full id: C4668_leiomyoblastoma_clear_retina_medulla_skin_lung_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr7:16505355..16505368,-p1@SOSTDC1
Hg19::chr7:16505416..16505438,-p2@SOSTDC1
Hg19::chr7:16505440..16505468,-p3@SOSTDC1


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.08e-33115
neurectoderm6.97e-2690
neural plate8.38e-2686
presumptive neural plate8.38e-2686
regional part of nervous system2.67e-2594
nervous system2.67e-2594
neural tube1.01e-2457
neural rod1.01e-2457
future spinal cord1.01e-2457
neural keel1.01e-2457
central nervous system4.34e-2382
anterior region of body7.55e-23129
craniocervical region7.55e-23129
head1.58e-22123
regional part of brain3.35e-2259
ectoderm2.68e-21173
presumptive ectoderm2.68e-21173
ectoderm-derived structure6.27e-21169
brain2.28e-2069
future brain2.28e-2069
pre-chordal neural plate1.68e-1961
anterior neural tube3.97e-1942
cerebral cortex1.35e-1825
pallium1.35e-1825
regional part of forebrain1.35e-1841
forebrain1.35e-1841
future forebrain1.35e-1841
telencephalon2.50e-1834
regional part of cerebral cortex6.49e-1822
gray matter6.54e-1834
brain grey matter6.54e-1834
regional part of telencephalon1.24e-1733
cerebral hemisphere3.22e-1732
multi-tissue structure4.77e-17347
neocortex9.15e-1720
organism subdivision1.11e-10365
organ1.64e-10511
organ part1.94e-10219
embryo9.48e-10612
epithelium6.80e-09309
cell layer9.54e-09312
multi-cellular organism1.45e-08659
embryonic structure8.37e-08605
developing anatomical structure8.37e-08605
gastrointestinal system1.68e-0735
germ layer1.87e-07604
embryonic tissue1.87e-07604
presumptive structure1.87e-07604
epiblast (generic)1.87e-07604
anatomical conduit2.46e-07241
anatomical cluster2.95e-07286
temporal lobe2.96e-077
anatomical system5.19e-07625
anatomical group6.50e-07626
posterior neural tube8.20e-0715
chordal neural plate8.20e-0715


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
GTF2B#2959331.94382993432423.06634405746243e-050.000629661633931024



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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