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Coexpression cluster:C2148: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511322511624479!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.015032688532929!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254652150530131!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185571636090697!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319851193913394!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195686530219825!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794443938953056!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032128175390236
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00511322511624479!FOXA1#3169;3:8.31106481203909:0.00274013818210985:0.015032688532929!GTF2B#2959;2:15.9719149671621:0.00563658572353722:0.0254652150530131!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185571636090697!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0319851193913394!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195686530219825!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.00794443938953056!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032128175390236
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57,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,0.12751,0.0438521,0.00283228,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0922008,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.0139335,0.36316,0.0625685,0.124464,0.544477,0.173134,0.101893,0.0107308,0.0149091,0.0155918,0.20386,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.0102393,0.415079,0.278645,0.365775,0.155708,0.248017,0.22995,0.0227764,0.0760151,0.0629459,0.143933,0.0803251,0.226641,0.0832234,0.0939463,0.0457255,0.367925,0.0471607,0.163865,0.226359,0.000140721,7.44804e-06,0.0388045,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.0345492,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.246601,0.193021,0.0153391,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.291976,0.320355,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.06079,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,0.0164195,0.0780061,0.315336,0.230477,0.279823,0.295555,0.154895,0.0420826,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.0368787,0.459091,0.54832,0.154964,0.296013,0.282366,0.537932,0.459994,0.523209,0.548059,0.25423,0.146971,0.45013,0.500698,0.472542,0.111549,0.399934,0.174869,0.509113,0.483077,0.224887,0.603763,0.541914,0.0778742,0.00233402,0.00207528,0.290703,0.254935,0.366999,0.139104,0.360199,0.0690757,0.657141,0.253797,0.365494,0.212703,0.56318,0.364079,0.315494,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.0529131,0.142433,0.261345,0.19941,0.209437,0.11765,0.401218,0.232518,0.0662179,0.12974,0.0184382,0.579004,0.000276195,0.113944,0.00419679,0.261575,0.0365695,0.264245,0.379063,0.326516,0.522925,0.436016,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.0999766,0.39549,0.234254,0.357409,0.86719,0.721266,0.50338,0.0746831,0.404625,0.172147,0.424691,0.357704,0.479581,0.259048,0.00679433,0.642173,0.284496,0.512545,0.512178,0.0102074,0.260945,0.321001,0.263302,0.552023,0.180735,0.00434967,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.260097,0.503881,0.454761,0.271678,0.142363,0.122467,0.301581,0.261657,0.346776,0.466529,0.545655,0.438176,0.349112,0.155207,0.385425,0.307816,0.461541,0.386339,0.382854,0.0650585,0.478745,0.611661,0.319747,0.136743,0.197104,0.241014,0.282281,0.612712,0.2536,0.246827,0.564333,0.12664,0.387134,0.559969,0.358813,0.668972,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.447581,0.0187686,0.254628,0.355111,0.139532,0.416962,0.632833,0.378333,0.152547,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.321224,0.469461,0.325254,0.266651,0.187728,0.231754,0.249415,0.283107,0.285648,0.10809,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.353147,0.112422,0.170886,0.267687,0.0560879,0.284866,0.0887542,0.267811,0.0651578,0.147872,0.189388,0.293546,0.210125,0.292967,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.0617695,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0612213,0.0627948,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.0604859,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.0371525,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0944985,0.332746,0.271338,0.242121,0.0498554,0.0326468,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0805224,0.0109087,0.111581,0.184359,0.334474,0.325785,0.257476,0.291176,0.081972,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.00786668,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.0675312,0.0936726,0.343425,0.132374,0.045178,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.620826,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.462021,0.706765,0.867962,0.905351,1.89595,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.297585,1.63433,1.09415,0.433165,0.344471,2.14358,0.285913,1.23038,0.740899,0.463978,0.371755,0.493145,1.59701,0.539378,0.53106,0.648765,1.49501,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,1.90242,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,1.98423,1.32819,0.893276,0.859396,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,1.72726,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,2.16273,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,1.28386,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,1.23342,3.0147,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,1.4628,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.644569
}}
}}

Revision as of 15:19, 26 November 2012


Full id: C2148_Eosinophils_CD4_CD19_Neutrophils_CD14_Basophils_CD14CD16



Phase1 CAGE Peaks

Hg19::chr11:62607111..62607161,+p@chr11:62607111..62607161
+
Hg19::chr13:98086167..98086226,-p1@AY726569
Hg19::chr18:19180794..19180824,+p@chr18:19180794..19180824
+
Hg19::chr4:78741549..78741569,+p@chr4:78741549..78741569
+


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
leukocyte1.21e-39136
hematopoietic cell3.98e-34177
hematopoietic stem cell4.25e-34168
angioblastic mesenchymal cell4.25e-34168
hematopoietic lineage restricted progenitor cell1.80e-31120
nongranular leukocyte1.29e-30115
hematopoietic oligopotent progenitor cell1.36e-30161
hematopoietic multipotent progenitor cell1.36e-30161
myeloid leukocyte8.66e-1872
nucleate cell4.20e-1755
classical monocyte4.87e-1742
CD14-positive, CD16-negative classical monocyte4.87e-1742
lymphoid lineage restricted progenitor cell1.22e-1652
lymphocyte1.32e-1653
common lymphoid progenitor1.32e-1653
myeloid cell2.17e-14108
common myeloid progenitor2.17e-14108
granulocyte monocyte progenitor cell4.81e-1467
myeloid lineage restricted progenitor cell6.03e-1466
macrophage dendritic cell progenitor1.12e-1361
defensive cell1.19e-1348
phagocyte1.19e-1348
monopoietic cell9.12e-1359
monocyte9.12e-1359
monoblast9.12e-1359
promonocyte9.12e-1359
mature alpha-beta T cell1.08e-1018
alpha-beta T cell1.08e-1018
immature T cell1.08e-1018
mature T cell1.08e-1018
immature alpha-beta T cell1.08e-1018
T cell2.10e-0825
pro-T cell2.10e-0825
B cell4.64e-0814
lymphocyte of B lineage6.03e-0824
pro-B cell6.03e-0824
CD8-positive, alpha-beta T cell2.59e-0711
intermediate monocyte5.94e-079
CD14-positive, CD16-positive monocyte5.94e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.96e-1998
blood island1.96e-1998
hemolymphoid system4.20e-18108
immune system2.02e-1393
bone marrow1.12e-1276
bone element9.06e-1282
skeletal element3.75e-0990
adult organism4.21e-09114
neural tube1.76e-0756
neural rod1.76e-0756
future spinal cord1.76e-0756
neural keel1.76e-0756
regional part of nervous system2.53e-0753
regional part of brain2.53e-0753
skeletal system6.40e-07100


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#90546.336201576962630.0006203100587215640.00511322511624479
FOXA1#316938.311064812039090.002740138182109850.015032688532929
GTF2B#2959215.97191496716210.005636585723537220.0254652150530131
HEY1#2346244.040111043105710.00375304636917980.0185571636090697
IRF1#365935.727872815172930.008097114790333330.0319851193913394
REST#597837.237521537096020.004104697304192610.0195686530219825
SIN3A#2594245.408884726815140.001168172384885160.00794443938953056
TAF1#687243.343046285745290.008005664898701650.032128175390236



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.