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Difference between revisions of "Coexpression cluster:C3723"

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|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139149252946022!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189916544682295!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115185542942615!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660185228094452!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325124856941144!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321995431881163!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914751219942148!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462010010830071!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255657649265593!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058103359005598!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.01540270127441!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108651688583692!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015668236517673!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018639731415405!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294324208648395!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000737398304986264!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269478092320426!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245698320969458!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000604919280665343!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470933492110122!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172832083725471!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881811442699286!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663841329887131!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767064605006275!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276533027454203!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246327016674283!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000939578071370626!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542565550560988!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629079939148467!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613418649364031!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019016704017331!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329182717662278!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140105158496572!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242652835731305!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109353013934451
 
|tf_chipseq_enrich=BCLAF1#9774;3:21.6526476101218:9.8473954032885e-05:0.00139149252946022!CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189916544682295!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115185542942615!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00660185228094452!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325124856941144!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321995431881163!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914751219942148!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0462010010830071!ELK4#2005;3:16.235681658468:0.000233604395574599:0.00255657649265593!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0058103359005598!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.01540270127441!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108651688583692!JUND#3727;3:6.99466394187103:0.00292184504273499:0.015668236517673!MAX#4149;3:6.45255550900712:0.00372191383426551:0.018639731415405!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0294324208648395!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000737398304986264!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269478092320426!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00245698320969458!NR2C2#7182;3:32.6146109052409:2.88098172333076e-05:0.000604919280665343!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00470933492110122!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172832083725471!POU2F2#5452;3:9.10612405774252:0.00132416519268213:0.00881811442699286!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00663841329887131!REST#5978;3:9.65002871612802:0.00111263624711459:0.00767064605006275!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0276533027454203!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0246327016674283!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000939578071370626!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00542565550560988!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00629079939148467!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00613418649364031!USF1#7391;3:6.36149927720796:0.0038840405729056:0.019016704017331!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329182717662278!ZBTB7A#51341;3:7.3519093078759:0.00251625586028227:0.0140105158496572!ZEB1#6935;3:16.8884320175439:0.000207548691732758:0.00242652835731305!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109353013934451
 
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145999,0.0656973,0.211746,0.220538,0.0801488,0.0757897,0.161801,0.193215,0.0549034,0.0779715,0.0561838,0.0417636,0.0345419,0.0388736,0.254674,0.170307,0.201033,0.0488949,0.174921,0.370421,0.0330727,0.348757,0.219556,0.0394698,0.0596469,0.419264,0.122476,0.108872,0.11002,0.26144,0.0286025,0.549354,0.144567,0.038848,0.0874516,0.0550279,0.144067,0.253693,0.217069,0.190048,0.131088,0.394069,0.237101,0.00501606,0.0761239,0.172491,0.0818785,0.182701,0.335058,0.147698,0.141463,0.167267,0.140622,0.0889592,0.309588,0.28711,0.0473033,0.094881,0.118532,0.132886,0.0774373,0.109194,0.128564,0.131452,0.687347,0.448776,0.051838,0.0993999,0.0500365,0.061829,0.0755121,0.0936516,0.144075,0.0340203,0.0741807,0.277091,0.739716,0.655293,0.21727,0.289306,0.119215,0.192475,0.177967,0.547859,0.057571,0.047591,0.392974,0.0608699,0.175319,0.300597,0.0713214,0.223874,0.291114,0.0355833,0.125606,0.175094,0.911304,0.297678,0.206454,0.218192,0.108277,0.0673484,0.108748,0.0494066,0.0958493,0.205732,0.0755808,0.045654,0.110216,0.070276,0.226171,0.153469,0.0376916,0.13262,0.0450031,0.0539144,0.114242,0.0929549,0.172425,0.104948,0.221645,0.057168,0.234298,0.0759837,0.286863,0.152372,0.0203723,0.0257725,0.101607,0.327067,0.172982,0.340936,0.151597,0.0626744,0.191335,0.148574,0.034431,0.155821,0.0718905,0.0919008,0.0602373,0.144304,0.15063,0.0973823,0.15503,0.170295,0.193653,0.137219,0.228144,0.251466,0.288096,0.11903,0.0838874,0.331451,0.113145,0.112651,0.186638,0.174776,0.0948451,0.264079,0.249049,0.140533,0.0997756,0.00352872,0.103667,0.113069,0.025556,0.16791,0.09066,0.585505,0.166967,0.188651,0.0813902,0.184948,0.156261,0.311847,0.511859,0.0590944,0.247324,0.178389,0.218229,0.231073,0.0972686,0.619906,0.0360851,0.412187,0.131093,0.0434602,0.133616,0.418146,0.0785808,0.449036,0.407369,0.231447,0.544776,0.115047,0.37006,0.42622,0.448797,0.197484,0.396996,0.36145,0.406019,0.381071,0.057779,0.643768,0.432035,0.138468,0.390366,0.48809,0.50058,0.443185,0.169835,0.875915,0.871256,0.227104,0.166658,0.617852,0.38649,0.284625,0.504757,0.55194,0.375373,0.28907,0.164197,0.462688,0.287881,0.574635,0.478174,0.336276,0.468444,0.258219,0.446557,0.243383,0.442897,0.390974,0.73485,0.109758,0.161598,0.751174,0.644754,0.496032,0.476802,0.37357,0.454657,0.477353,0.452741,0.746954,0.771991,0.20342,0.200493,0.20558,0.300504,0.0361545,0.425963,0.349197,0.383291,0.156104,0.141318,0.0168417,0.0961477,0.314438,0.354789,0.163828,0.230581,0.120226,0.28424,0.20075,0.314429,0.181415,0.282286,0.446891,0.616388,0.408413,0.516511,0.322213,0.656109,0.33942,0.61031,0.387276,0.522605,0.802166,0.180745,0.222037,0.416621,0.416292,0.128937,0.734551,0.215157,0.204817,0.452428,0.138871,0.673493,0.166905,0.19783,0.0833851,0.316453,0.48065,0.175199,0.332919,0.373557,0.523625,0.408861,0.365487,0.534741,0.39088,0.363192,0.0303438,0.203486,0.273398,0.375787,0.4466,0.351067,0.275347,0.269604,0.305885,0.241132,0.371414,0.30666,0.303709,0.495883,0.386538,0.035296,0.250964,0.0131557,0.457886,0.504711,0.220231,0.509064,0.196976,0.191517,0.463751,0.601877,0.307334,0.459728,0.283463,0.563586,0.472935,0.399569,0.273281,0.368095,0.275089,0.384593,0.47795,0.359231,0.339729,0.197805,0.608187,0.387069,0.332774,0.52832,0.299887,0.634365,0.205413,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.18966,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,0.163057,0.219428,0.208013,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.179412,0.193601,0.220904,0.222977,0.341681,0.0542164,0.21801,0.198614,0.186804,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.27872,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.168748,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.259632,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.0367308,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.249101,0.115972,0.224568,0.246105,0.173026,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.0269005,0.172134,0.176789,0.0969345,0.00162178,0.310405,0.280943,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.0577193,0.261724,0.211332,0.187731,0.233626,0.189559,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.0497481,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.00475042,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435
 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,2.64303,0.575162,0.452865,0.305559,0.69094,1.95727,0.845342,0.635379,0.743951,1.00973,1.85641,0.842925,2.63304,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,2.47502,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,1.7986,0.502203,0.886337,1.45054,0.430728,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.95969,0.303648,0.381882,2.39382,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,2.61709,2.12604,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,0.698641,1.37083,1.21015,0.941179,1.78371,1.03563,0.624795,0.744018,1.69223,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224
 
}}
 
}}

Revision as of 07:18, 26 November 2012


Full id: C3723_nonsmall_globus_spinal_medulla_thalamus_pineal_brain



Phase1 CAGE Peaks

  Short description
Hg19::chr18:47013532..47013544,- p3@C18orf32
Hg19::chr18:47013564..47013585,- p2@C18orf32
Hg19::chr18:47013586..47013633,- p1@C18orf32


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Uber Anatomy
Ontology termp-valuen
neural tube8.18e-2856
neural rod8.18e-2856
future spinal cord8.18e-2856
neural keel8.18e-2856
regional part of nervous system7.65e-2653
regional part of brain7.65e-2653
central nervous system7.84e-2281
regional part of forebrain1.52e-2141
forebrain1.52e-2141
anterior neural tube1.52e-2141
future forebrain1.52e-2141
adult organism1.83e-21114
neural plate8.97e-2182
presumptive neural plate8.97e-2182
brain6.48e-2068
future brain6.48e-2068
nervous system1.09e-1989
neurectoderm3.82e-1986
brain grey matter1.56e-1734
gray matter1.56e-1734
telencephalon1.99e-1734
regional part of telencephalon2.41e-1632
cerebral hemisphere2.68e-1632
pre-chordal neural plate3.44e-1561
bone marrow4.49e-1576
ecto-epithelium5.75e-14104
regional part of cerebral cortex6.09e-1322
bone element1.47e-1282
cerebral cortex1.91e-1225
pallium1.91e-1225
neocortex8.41e-1220
hematopoietic system1.08e-1198
blood island1.08e-1198
skeletal element8.11e-1190
structure with developmental contribution from neural crest8.26e-11132
immune system1.28e-1093
hemolymphoid system1.95e-10108
tube4.53e-10192
skeletal system2.90e-09100
developing anatomical structure9.01e-09581
embryonic structure2.86e-08564
germ layer9.71e-08560
germ layer / neural crest9.71e-08560
embryonic tissue9.71e-08560
presumptive structure9.71e-08560
germ layer / neural crest derived structure9.71e-08560
epiblast (generic)9.71e-08560
posterior neural tube1.84e-0715
chordal neural plate1.84e-0715
organ3.73e-07503
embryo6.17e-07592


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
BCLAF1#9774321.65264761012189.8473954032885e-050.00139149252946022
CCNT2#90536.336201576962630.003930750035764890.0189916544682295
CEBPB#105137.971147625824820.001974187055288560.0115185542942615
CHD2#1106310.34402283411690.0009033701102746880.00660185228094452
E2F1#186934.907389214879320.008460985347239390.0325124856941144
E2F6#187635.017155731697390.00791769806886330.0321995431881163
EBF1#187938.9064668465690.00141523283560980.00914751219942148
ELF1#199734.258097958807540.01295179875054610.0462010010830071
ELK4#2005316.2356816584680.0002336043955745990.00255657649265593
FOXA1#3169311.08141974938550.000734755275698670.0058103359005598
GABPB1#255337.067683836182170.002832212825417420.01540270127441
HMGN3#932438.178547723350590.001827766942164210.0108651688583692
JUND#372736.994663941871030.002921845042734990.015668236517673
MAX#414936.452555509007120.003721913834265510.018639731415405
MYC#460935.22228187160940.007020843755740150.0294324208648395
NANOG#79923329.24477848101273.99627955670032e-050.000737398304986264
NFKB1#479035.488063424193840.006049381815655430.0269478092320426
NFYB#4801316.75979325353650.0002123649923296180.00245698320969458
NR2C2#7182332.61461090524092.88098172333076e-050.000604919280665343
NRF1#4899312.21027944771090.0005492172401020010.00470933492110122
PAX5#507936.669565531177830.003370290999677260.0172832083725471
POU2F2#545239.106124057742520.001324165192682130.00881811442699286
RAD21#5885310.35503389545630.0009004912073565420.00663841329887131
REST#597839.650028716128020.001112636247114590.00767064605006275
SIN3A#2594235.408884726815140.006318961977991520.0276533027454203
SP1#666735.69838137814090.005403962701712170.0246327016674283
SP2#6668326.15353049384465.58768218891694e-050.000939578071370626
TAF7#6879311.43306940492390.0006690181981945830.00542565550560988
TCF12#6938310.63446490218640.0008313523990202070.00629079939148467
TCF7L2#6934310.77017656313730.0008003181298398380.00613418649364031
USF1#739136.361499277207960.00388404057290560.019016704017331
YY1#752834.911170749853860.008441455341808260.0329182717662278
ZBTB7A#5134137.35190930787590.002516255860282270.0140105158496572
ZEB1#6935316.88843201754390.0002075486917327580.00242652835731305
ZNF263#1012738.221841637010680.001799043925565870.0109353013934451



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.