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Coexpression cluster:C1411: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;5:7.42205570547417:9.7002838805275e-05:0.00137985283056172!IRF4#3662;5:18.2620939056201:1.14070523243612e-06:4.66095906769937e-05!MEF2A#4205;4:12.495487273096:0.000111333627719979:0.00154601419298589!MEF2C#4208;2:13.7704514975413:0.00823559694227006:0.0324670658709702!NFKB1#4790;6:5.48806342419384:3.65870229532191e-05:0.000707351368050953!PAX5#5079;5:5.55797127598152:0.000397717619661286:0.00388670632355245!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.038020117083685!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188565372066352!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280012989295929!TCF12#6938;5:8.86205408515535:4.06365504449859e-05:0.000743524998585123!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.00204824897369564
|tf_chipseq_enrich=EBF1#1879;5:7.42205570547417:9.7002838805275e-05:0.00137985283056172!IRF4#3662;5:18.2620939056201:1.14070523243612e-06:4.66095906769937e-05!MEF2A#4205;4:12.495487273096:0.000111333627719979:0.00154601419298589!MEF2C#4208;2:13.7704514975413:0.00823559694227006:0.0324670658709702!NFKB1#4790;6:5.48806342419384:3.65870229532191e-05:0.000707351368050953!PAX5#5079;5:5.55797127598152:0.000397717619661286:0.00388670632355245!POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.038020117083685!SPI1#6688;5:6.83693625710227:0.000144964177397403:0.00188565372066352!SRF#6722;3:6.8985891310839:0.0064424516893037:0.0280012989295929!TCF12#6938;5:8.86205408515535:4.06365504449859e-05:0.000743524998585123!ZEB1#6935;4:11.2589546783626:0.000167270037980545:0.00204824897369564
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9,0.31161,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.0228216,0.207936,0.454529,0.0563868,0.796918,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.264969,0.417985,0.491614,0.146453,0.315229,0.157053,0.332022,0.557852,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.410665,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.749878,0.881177,0.387334,0.494914,0.224219,0.347904,0.324262,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.531917,0.912024,0.370285,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.754571,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.404239,0.439697,0.493192,0.223892,0.160738,0.553042,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.828194,0.306056,0.341713,0.156156,0.33569,0.288104,0.526446,0.419951,0.114697,0.433479,0.324956,0.388835,0.408751,0.648685,0.576023,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.60218,0.696439,0.281293,0.409327,0.792771,0.322166,0.603176,0.670776,0.334228,0.355968,0.636386,0.592254,0.27962,0.616927,0.518189,0.15467,0.312447,0.725074,0.628346,0.0471089,0.163758,0.689958,0.772379,0.405032,0.91547,0.402631,0.768239,0.853963,0.623606,0.488239,0.410034,0.799242,0.735002,0.494578,0.301433,0.129825,0.492887,0.509735,0.727698,0.559471,0.717449,0.449761,0.6937,0.427531,0.950427,0.629087,0.929695,0.899649,0.297082,0.938085,0.8738,0.397935,0.830195,0.607585,0.953814,0.0105885,0.810134,0.935968,0.794297,0.36546,0.360788,0.368898,0.510705,0.447298,0.304675,0.212589,0.619669,0.287839,0.262665,0.654187,0.183051,0.530004,0.218878,0.300816,0.407994,0.225997,0.487688,0.0862754,0.175134,0.329919,0.143177,0.583109,0.0137273,0.650025,0.426477,0.183267,0.167995,0.563634,0.561918,0.624569,0.772094,0.960862,0.785953,0.394773,0.292847,0.0949382,0.0375679,0.929537,0.251325,0.0778516,0.700165,0.258457,0.654742,0.052476,0.356524,0.159817,0.532764,0.730276,0.319704,0.555004,0.240491,0.773067,0.650555,0.231104,0.783534,0.628973,0.594475,0.416321,0.365565,0.47205,0.24311,0.331346,0.0571946,0.474879,0.601828,0.518205,0.424119,0.00267752,0.519279,0.16418,0.745866,0.255881,0.757999,0.438945,0.003174,0.706112,0.754688,0.39196,0.172059,0.355152,0.346355,0.354044,0.280648,0.520214,0.708106,0.486574,0.493703,0.722202,0.639482,0.471879,0.600697,0.474504,0.621275,0.373171,0.223923,0.564042,0.356483,0.28925,0.624316,0.55481,0.191884,0.509842,0.597297,0.0782868,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.613566,0.445744,0.371991,0.332112,0.326635,0.349721,0.39301,0.396235,0.566617,0.524829,0.388491,0.357781,0.338712,0.231439,0.0739965,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.0963341,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.0755244,0.578088,0.285875,0.225945,0.018816,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.122302,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.00847093,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.0557026,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.442751,0.323763,0.486842,0.458912,0.033144,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.0877682,0.397562,0.21727,0.351946,0.345508,0.0296607,0.486223,0.437432,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.132855,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.116282,0.369492,0.226443
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.262261,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.892779,0.664996,0.127969,0.436569,0.6169,0.576478,0.387783,0.483957,0.730467,0.585619,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.640661,0.35719,0.0334022,0.35388,0.585658,0.878269,0.248856,0.355745,0.513952,0.0979105,0.390088,0.636689,0.468392,0.66382,0.542147,0.304272,1.02586,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,0.186533,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.75612,0.146905,1.15727,0.218784,0.594475,0.192925,0.84426,0.913168,0.477584,0.676305,0.86037,0.684313,1.37357,1.10535,0.0481066,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.234532,0.987239,0.776336,0.166235,0.881389,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,0.44815,0.978783,0.430775,0.563054,1.29401,0.928633,0.800507,0.529546,0.824029,0.840396,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.324369,1.07876,1.32127,1.20639,0.692462,1.35529,0.520084,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.136746,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,1.21528,0.454152,1.27379,1.06043,0.912368,1.1583,0.83286,0.683502,0.79772,0.661335,0.521461
}}
}}

Revision as of 14:52, 26 November 2012


Full id: C1411_immature_Dendritic_CD19_Mast_CD14_Neutrophils_CD34



Phase1 CAGE Peaks

Hg19::chr15:74677677..74677688,+p@chr15:74677677..74677688
+
Hg19::chr15:74677699..74677722,+p@chr15:74677699..74677722
+
Hg19::chr15:74689107..74689118,+p@chr15:74689107..74689118
+
Hg19::chr16:22218470..22218480,-p@chr16:22218470..22218480
-
Hg19::chr17:7154288..7154306,+p@chr17:7154288..7154306
+
Hg19::chr2:224701010..224701027,+p@chr2:224701010..224701027
+


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
leukocyte1.70e-39136
hematopoietic stem cell4.11e-33168
angioblastic mesenchymal cell4.11e-33168
hematopoietic cell1.30e-30177
hematopoietic oligopotent progenitor cell2.65e-26161
hematopoietic multipotent progenitor cell2.65e-26161
hematopoietic lineage restricted progenitor cell3.34e-21120
lymphoid lineage restricted progenitor cell2.03e-1952
lymphocyte6.39e-1953
common lymphoid progenitor6.39e-1953
nucleate cell5.57e-1855
nongranular leukocyte5.38e-17115
granulocyte1.18e-148
lymphocyte of B lineage4.85e-1424
pro-B cell4.85e-1424
dendritic cell9.15e-1310
histamine secreting cell1.79e-125
biogenic amine secreting cell1.79e-125
granulocytopoietic cell1.79e-125
mast cell1.79e-125
mast cell progenitor1.79e-125
basophil mast progenitor cell1.79e-125
mesenchymal cell3.03e-12354
connective tissue cell1.09e-11361
Langerhans cell2.98e-115
blood cell2.70e-1011
myeloid cell7.08e-10108
common myeloid progenitor7.08e-10108
motile cell9.46e-10386
myeloid leukocyte1.01e-0972
conventional dendritic cell9.14e-098
plasmacytoid dendritic cell1.19e-083
intermediate monocyte1.59e-089
CD14-positive, CD16-positive monocyte1.59e-089
stem cell2.74e-08441
basophil3.18e-083
neutrophil3.58e-083
single nucleate cell8.47e-083
mononuclear cell8.47e-083
natural killer cell1.09e-073
pro-NK cell1.09e-073
multi fate stem cell1.97e-07427
somatic stem cell4.07e-07433
Uber Anatomy
Ontology termp-valuen
connective tissue1.51e-11371
hematopoietic system4.49e-0798
blood island4.49e-0798


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
EBF1#187957.422055705474179.7002838805275e-050.00137985283056172
IRF4#3662518.26209390562011.14070523243612e-064.66095906769937e-05
MEF2A#4205412.4954872730960.0001113336277199790.00154601419298589
MEF2C#4208213.77045149754130.008235596942270060.0324670658709702
NFKB1#479065.488063424193843.65870229532191e-050.000707351368050953
PAX5#507955.557971275981520.0003977176196612860.00388670632355245
POLR2A#543062.147453176558070.01019570676818780.038020117083685
SPI1#668856.836936257102270.0001449641773974030.00188565372066352
SRF#672236.89858913108390.00644245168930370.0280012989295929
TCF12#693858.862054085155354.06365504449859e-050.000743524998585123
ZEB1#6935411.25895467836260.0001672700379805450.00204824897369564



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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