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Coexpression cluster:C4062: Difference between revisions

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|ontology_enrichment_disease=DOID:0050687!2.09e-21!143;DOID:162!9.28e-17!235;DOID:14566!1.29e-15!239;DOID:305!1.38e-15!106
|ontology_enrichment_disease=DOID:0050687!2.09e-21!143;DOID:162!9.28e-17!235;DOID:14566!1.29e-15!239;DOID:305!1.38e-15!106
|ontology_enrichment_uberon=UBERON:0005743!1.21e-26!86;UBERON:0000073!2.76e-25!94;UBERON:0001016!2.76e-25!94;UBERON:0001017!1.01e-24!82;UBERON:0000955!9.88e-21!69;UBERON:0006238!9.88e-21!69;UBERON:0001049!1.71e-20!57;UBERON:0005068!1.71e-20!57;UBERON:0006241!1.71e-20!57;UBERON:0007135!1.71e-20!57;UBERON:0002346!2.58e-20!90;UBERON:0003075!3.38e-19!86;UBERON:0007284!3.38e-19!86;UBERON:0002780!9.10e-18!41;UBERON:0001890!9.10e-18!41;UBERON:0006240!9.10e-18!41;UBERON:0002616!1.85e-17!59;UBERON:0007023!1.92e-17!115;UBERON:0003080!7.16e-17!42;UBERON:0000924!6.03e-16!173;UBERON:0006601!6.03e-16!173;UBERON:0004121!5.69e-15!169;UBERON:0001893!1.26e-14!34;UBERON:0002020!1.61e-14!34;UBERON:0003528!1.61e-14!34;UBERON:0001869!3.73e-14!32;UBERON:0002791!4.13e-14!33;UBERON:0003056!2.55e-13!61;UBERON:0000033!3.35e-12!123;UBERON:0000956!4.55e-12!25;UBERON:0000203!4.55e-12!25;UBERON:0002619!8.64e-12!22;UBERON:0001950!2.60e-11!20;UBERON:0000153!2.64e-11!129;UBERON:0007811!2.64e-11!129;UBERON:0000025!3.17e-09!194;UBERON:0004111!5.17e-09!241;UBERON:0000481!2.20e-08!347;UBERON:0000064!9.42e-08!219;UBERON:0000475!1.12e-07!365;UBERON:0000477!1.28e-07!286;UBERON:0000062!3.61e-07!511;UBERON:0000483!3.77e-07!309
|ontology_enrichment_uberon=UBERON:0005743!1.21e-26!86;UBERON:0000073!2.76e-25!94;UBERON:0001016!2.76e-25!94;UBERON:0001017!1.01e-24!82;UBERON:0000955!9.88e-21!69;UBERON:0006238!9.88e-21!69;UBERON:0001049!1.71e-20!57;UBERON:0005068!1.71e-20!57;UBERON:0006241!1.71e-20!57;UBERON:0007135!1.71e-20!57;UBERON:0002346!2.58e-20!90;UBERON:0003075!3.38e-19!86;UBERON:0007284!3.38e-19!86;UBERON:0002780!9.10e-18!41;UBERON:0001890!9.10e-18!41;UBERON:0006240!9.10e-18!41;UBERON:0002616!1.85e-17!59;UBERON:0007023!1.92e-17!115;UBERON:0003080!7.16e-17!42;UBERON:0000924!6.03e-16!173;UBERON:0006601!6.03e-16!173;UBERON:0004121!5.69e-15!169;UBERON:0001893!1.26e-14!34;UBERON:0002020!1.61e-14!34;UBERON:0003528!1.61e-14!34;UBERON:0001869!3.73e-14!32;UBERON:0002791!4.13e-14!33;UBERON:0003056!2.55e-13!61;UBERON:0000033!3.35e-12!123;UBERON:0000956!4.55e-12!25;UBERON:0000203!4.55e-12!25;UBERON:0002619!8.64e-12!22;UBERON:0001950!2.60e-11!20;UBERON:0000153!2.64e-11!129;UBERON:0007811!2.64e-11!129;UBERON:0000025!3.17e-09!194;UBERON:0004111!5.17e-09!241;UBERON:0000481!2.20e-08!347;UBERON:0000064!9.42e-08!219;UBERON:0000475!1.12e-07!365;UBERON:0000477!1.28e-07!286;UBERON:0000062!3.61e-07!511;UBERON:0000483!3.77e-07!309
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279917096206132!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325940337383473!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0322862903566302!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00916111950652364!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463069703094137!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00391753763782668!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294963554851662!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614636555352179!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140457106249075
|tfbs_overrepresentation=0.147255,0.0586687,0.35968,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.139423,0.225367,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.204953,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.00381532,0.167053,0.378921,0.00234364,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,6.2605e-08,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.00212123,0.153631,0.0927458,0.27413,0.0574857,0.276221,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.338096,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.101221,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,4.57719e-05,0.0693171,0.0988228,0.0842275,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.569726,0.384785,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.0085789,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.003405,0.446759,0.0865903,0.0380459,0.130174,0.059488,0.000318664,0.00485874,0.0821962,0.563047,8.37562e-05,2.60602e-13,0.335423,0.629514,0.261553,0.446302,0.373681,0.309233,0.49143,0.330703,0.395854,0.329568,0.042539,0.615744,0.271958,0.292154,0.405773,0.39729,0.581713,0.597171,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.647576,0.528324,0.520763,0.370782,0.415647,0.0297533,0.253571,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.21363,0.291709,0.448095,0.576651,0.416816,0.292835,0.476744,0.439556,0.373868,0.213592,0.608919,0.18237,0.126021,4.6495e-09,0.747852,0.275351,0.236471,0.185661,0.346319,0.179399,0.270984,0.625945,0.503058,0.0367769,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.00243366,0.000729888,0.217247,0.412837,0.305671,0.546839,0.551561,0.120021,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.0222308,0.589326,0.00568155,0.294698,0.34331,0.477304,0.289204,0.0077225,0.0295492,0.278044,0.000315884,0.428671,0.228096,0.336314,0.19763,0.15631,0.20495,0.421464,0.48267,0.420626,0.516462,2.25312e-08,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.405955,0.41707,0.363685,0.464871,2.2584e-06,0.206222,0.525396,0.651524,0.437176,0.269226,0.339277,0.192529,0.281425,0.141758,0.455379,0.520495,0.159617,0.238587,0.372281,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.0769581,0.347298,0.539392,0.34988,0.475069,0.404569,0.0847452,0.630264,0.0562865,0.0697683,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.203656,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,4.58666e-08,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.210369,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.406014,0.127758,0.175785,0.184486,0.169234,0.0876426,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.173708,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,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}}
}}

Revision as of 11:48, 5 September 2012


Full id: C4062_argyrophil_somatostatinoma_MCF7_small_heart_neuroblastoma_cerebellum



Phase1 CAGE Peaks

Hg19::chr20:62130603..62130627,-p3@EEF1A2
Hg19::chr20:62130629..62130646,-p4@EEF1A2
Hg19::chr20:62130651..62130656,-p11@EEF1A2


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 cell3.94e-07254
Uber Anatomy
Ontology termp-valuen
regional part of nervous system2.76e-2594
nervous system2.76e-2594
central nervous system1.01e-2482
brain9.88e-2169
future brain9.88e-2169
neural tube1.71e-2057
neural rod1.71e-2057
future spinal cord1.71e-2057
neural keel1.71e-2057
neurectoderm2.58e-2090
neural plate3.38e-1986
presumptive neural plate3.38e-1986
regional part of forebrain9.10e-1841
forebrain9.10e-1841
future forebrain9.10e-1841
regional part of brain1.85e-1759
adult organism1.92e-17115
anterior neural tube7.16e-1742
ectoderm6.03e-16173
presumptive ectoderm6.03e-16173
ectoderm-derived structure5.69e-15169
telencephalon1.26e-1434
gray matter1.61e-1434
brain grey matter1.61e-1434
cerebral hemisphere3.73e-1432
regional part of telencephalon4.13e-1433
pre-chordal neural plate2.55e-1361
head3.35e-12123
cerebral cortex4.55e-1225
pallium4.55e-1225
regional part of cerebral cortex8.64e-1222
neocortex2.60e-1120
anterior region of body2.64e-11129
craniocervical region2.64e-11129
tube3.17e-09194
anatomical conduit5.17e-09241
multi-tissue structure2.20e-08347
organ part9.42e-08219
organism subdivision1.12e-07365
anatomical cluster1.28e-07286
organ3.61e-07511
epithelium3.77e-07309
Disease
Ontology termp-valuen
cell type cancer2.09e-21143
cancer9.28e-17235
disease of cellular proliferation1.29e-15239
carcinoma1.38e-15106


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
CTCF#1066435.360256373075030.0064925092527670.0279917096206132
E2F1#186934.907389214879320.008460985347239390.0325940337383473
E2F6#187635.017155731697390.00791769806886330.0322862903566302
EBF1#187938.9064668465690.00141523283560980.00916111950652364
ELF1#199734.258097958807540.01295179875054610.0463069703094137
HDAC2#3066313.41562023662630.0004140761399857210.00391753763782668
MYC#460935.22228187160940.007020843755740150.0294963554851662
TCF7L2#6934310.77017656313730.0008003181298398380.00614636555352179
ZBTB7A#5134137.35190930787590.002516255860282270.0140457106249075



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4062&oldid=2130582"