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Coexpression cluster:C2708: Difference between revisions

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|tf_chipseq_enrich=PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435113956272694!RAD21#5885;3:7.76627542159225:0.003341119385872:0.017271849108602!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765860169514542!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281083455910336!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483237404341906!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342546913771778!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976958872249289
|tf_chipseq_enrich=PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435113956272694!RAD21#5885;3:7.76627542159225:0.003341119385872:0.017271849108602!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765860169514542!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281083455910336!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483237404341906!ZBTB7A#51341;3:5.51393198090692:0.00903835282108109:0.0342546913771778!ZNF143#7702;3:10.1256574141709:0.00153486161068818:0.00976958872249289
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849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.0197215,0.184022,0.216557,0.182956,0.116818,0.389792,0.36316,0.0625685,0.124464,0.00856472,0.173134,0.101893,0.142875,0.167635,0.171311,0.787798,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.535567,0.758305,0.278645,0.011228,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.367925,0.0471607,0.163865,0.226359,0.960445,0.974549,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.459091,0.0466753,0.502211,0.296013,0.649813,0.181196,0.459994,0.523209,0.548059,0.25423,0.490559,0.45013,0.500698,0.135135,0.685908,0.747471,0.174869,0.818701,0.14198,0.590496,0.603763,0.541914,0.00346025,0.938109,0.934991,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.824761,0.365494,0.212703,0.201391,0.364079,0.680099,0.0119013,0.0181617,0.206595,0.000763941,0.545608,0.310552,0.865054,0.483764,0.829658,0.784052,0.209437,0.843495,0.401218,0.0651244,0.882403,0.464001,0.871271,0.579004,0.605327,0.839946,0.860705,0.0376583,0.257956,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.86719,0.365184,0.50338,0.252827,0.404625,0.416164,0.424691,0.715362,0.479581,0.62689,0.884725,0.0854676,0.284496,0.512545,0.512178,0.563206,0.829402,0.684899,0.263302,0.047857,0.180735,0.775168,0.216102,0.254659,0.109605,0.0924199,0.217863,0.226491,0.102502,0.463987,0.627953,0.503881,0.454761,0.271678,0.483658,0.452129,0.301581,0.0376831,0.346776,0.466529,0.545655,0.438176,0.349112,0.741477,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,0.0285097,0.24434,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.0333324,0.564333,0.70712,0.387134,0.198743,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.42505,0.254628,0.713293,0.479347,0.416962,0.264955,0.378333,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.0460393,0.231754,0.249415,0.283107,0.285648,0.427316,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.0429696,0.161712,0.237871,0.239139,0.095257,0.328852,0.0627948,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.0465068,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,2.93909,1.32255,0.739643,0.821651,0.395818,0.392841,0.902371,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,1.18986,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,1.33003,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,0.0946706,0.61613,0.822818,0.694903,3.80116,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,10.657,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,1.37313,0.465545,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.393155,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,1.98497,1.52813,5.95736,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,4.42116,5.05793,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
}}
}}

Revision as of 15:40, 26 November 2012


Full id: C2708_pineal_cerebellum_medulloblastoma_testis_olfactory_CD14_parietal



Phase1 CAGE Peaks

Hg19::chr2:97466889..97466899,+p@chr2:97466889..97466899
+
Hg19::chr2:97467009..97467037,+p@chr2:97467009..97467037
+
Hg19::chr2:97467069..97467087,+p@chr2:97467069..97467087
+
Hg19::chr2:97467585..97467621,+p@chr2:97467585..97467621
+


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><br>

Cell Type
Ontology termp-valuen
classical monocyte1.76e-0942
CD14-positive, CD16-negative classical monocyte1.76e-0942
defensive cell4.51e-0748
phagocyte4.51e-0748
Uber Anatomy
Ontology termp-valuen
neural tube7.26e-2856
neural rod7.26e-2856
future spinal cord7.26e-2856
neural keel7.26e-2856
regional part of nervous system3.10e-2653
regional part of brain3.10e-2653
regional part of forebrain7.93e-2441
forebrain7.93e-2441
anterior neural tube7.93e-2441
future forebrain7.93e-2441
brain8.66e-2368
future brain8.66e-2368
telencephalon1.52e-1934
brain grey matter1.74e-1934
gray matter1.74e-1934
neurectoderm2.41e-1986
central nervous system2.58e-1981
regional part of telencephalon2.29e-1832
adult organism2.35e-18114
neural plate2.88e-1882
presumptive neural plate2.88e-1882
cerebral hemisphere3.26e-1832
nervous system5.98e-1789
regional part of cerebral cortex2.26e-1422
cerebral cortex3.54e-1425
pallium3.54e-1425
pre-chordal neural plate7.39e-1461
neocortex5.08e-1320
ecto-epithelium7.17e-11104
organ system subdivision6.93e-08223
structure with developmental contribution from neural crest2.29e-07132
basal ganglion5.79e-079
nuclear complex of neuraxis5.79e-079
aggregate regional part of brain5.79e-079
collection of basal ganglia5.79e-079
cerebral subcortex5.79e-079
neural nucleus8.37e-079
nucleus of brain8.37e-079


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
PAX5#507935.002174148383370.01196533174786410.0435113956272694
RAD21#588537.766275421592250.0033411193858720.017271849108602
SMC3#9126311.28369963369960.001115802366868050.00765860169514542
SPI1#668836.153242631392040.006580387113059030.0281083455910336
USF1#739134.771124457905970.01370465887188020.0483237404341906
ZBTB7A#5134135.513931980906920.009038352821081090.0342546913771778
ZNF143#7702310.12565741417090.001534861610688180.00976958872249289



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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