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Coexpression cluster:C1351: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;3:12.1789008961518:0.0012598148712534:0.00846133796391212!EBF1#1879;4:5.93764456437934:0.00197515363642171:0.0114888928228486!FOS#2353;4:5.99863687259627:0.00189982371188635:0.0111827587581411!FOSL1#8061;2:13.2378599054577:0.0088883308800909:0.0337191568756198!GATA1#2623;3:6.78015407190022:0.00676576398334856:0.0287473403033743!GATA2#2624;4:8.49662115570266:0.000499302449761718:0.00440911884253522!JUN#3725;3:6.25641459616817:0.00848634685095487:0.032407238976448!MEF2A#4205;3:9.37161545482203:0.00268739994710391:0.0147985533626271!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438235030178419!SPI1#6688;4:5.46954900568182:0.0026973005361414:0.014840552665371
|tf_chipseq_enrich=BATF#10538;3:12.1789008961518:0.0012598148712534:0.00846133796391212!EBF1#1879;4:5.93764456437934:0.00197515363642171:0.0114888928228486!FOS#2353;4:5.99863687259627:0.00189982371188635:0.0111827587581411!FOSL1#8061;2:13.2378599054577:0.0088883308800909:0.0337191568756198!GATA1#2623;3:6.78015407190022:0.00676576398334856:0.0287473403033743!GATA2#2624;4:8.49662115570266:0.000499302449761718:0.00440911884253522!JUN#3725;3:6.25641459616817:0.00848634685095487:0.032407238976448!MEF2A#4205;3:9.37161545482203:0.00268739994710391:0.0147985533626271!NFKB1#4790;4:3.65870894946256:0.0120792728901523:0.0438235030178419!SPI1#6688;4:5.46954900568182:0.0026973005361414:0.014840552665371
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6,0.444489,0.31161,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.123916,0.0563868,0.796918,0.268235,0.0761868,0.167255,0.107028,0.267379,0.443026,0.387018,0.343977,0.244992,0.264969,0.417985,0.491614,0.146453,0.315229,0.157053,0.062493,0.557852,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.491788,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.902248,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.749878,0.358495,0.387334,0.494914,0.224219,0.347904,0.324262,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.161055,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.992133,0.99594,0.370285,0.388777,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.754571,0.287361,0.138613,0.175356,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.404239,0.115126,0.493192,0.223892,0.160738,0.193111,0.213489,0.212611,0.338443,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.525576,0.000555315,0.341713,0.156156,0.33569,0.288104,0.526446,0.761719,0.114697,0.433479,0.324956,0.388835,0.408751,0.648685,0.855529,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.60218,0.334542,0.648789,0.409327,0.466607,0.685907,0.603176,0.305003,0.696176,0.355968,0.0197115,0.592254,0.647186,0.249357,0.82397,0.611131,0.105986,0.0462498,0.0784335,0.0119872,0.750579,0.689958,0.772379,0.920342,0.983425,0.402631,0.429394,0.573004,0.623606,0.488239,0.754734,0.218104,0.926642,0.0320309,0.301433,0.711296,0.492887,0.245317,0.373476,0.559471,0.717449,0.449761,0.331289,0.427531,0.577777,0.629087,0.495268,0.668933,0.297082,0.938085,0.612581,0.397935,0.830195,0.607585,0.593416,0.72684,0.953275,0.935968,0.948012,0.36546,0.360788,0.0784093,0.510705,0.447298,0.10163,0.0562917,0.0742819,0.287839,0.262665,0.654187,0.183051,0.00746054,0.583703,0.300816,0.407994,0.225997,0.487688,0.230404,0.175134,0.329919,0.143177,0.359097,0.57085,0.282589,0.426477,0.540605,0.881739,0.201767,0.561918,0.624569,0.185857,0.960862,0.455987,0.0908572,0.659669,0.292434,0.129844,0.49471,0.251325,0.0114272,0.700165,0.258457,0.893393,0.305952,0.356524,0.159817,0.532764,0.730276,0.319704,0.555004,0.240491,0.773067,0.650555,0.0644796,0.783534,0.628973,0.594475,0.416321,0.365565,0.13482,0.610358,0.693748,0.578885,0.474879,0.868553,0.166381,0.424119,0.0676419,0.519279,0.16418,0.39773,0.623664,0.171067,0.438945,0.0742738,0.346229,0.167767,0.39196,0.416041,0.355152,0.346355,0.712437,0.54954,0.520214,0.708106,0.486574,0.493703,0.366382,0.639482,0.471879,0.600697,0.474504,0.253554,0.727464,0.0612483,0.564042,0.356483,0.28925,0.624316,0.55481,0.777518,0.509842,0.0537641,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,0.345583,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.246146,0.445744,0.371991,0.332112,0.326635,0.0698709,0.39301,0.396235,0.566617,0.524829,0.388491,0.357781,0.338712,0.0291267,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.479755,0.163801,0.245045,0.373321,0.433875,0.395243,0.130132,0.373481,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.465261,0.0755244,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.385234,0.291842,0.392097,0.352327,0.232997,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.360691,0.26003,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.180857,0.454949,0.378002,0.340219,0.412672,0.343186,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.36701,0.504058,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.0352084,0.442751,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.544575,0.21822,0.388558,0.397562,0.21727,0.351946,0.345508,0.484083,0.486223,0.437432,0.302171,0.0925994,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.177664,0.313891,0.292462,0.46896,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.441686,0.369492,0.592234
|tfbs_overrepresentation_for_novel_motifs=0.44418,0.333388,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.267027,0.262261,0.553339,0.707204,0.223349,0.650887,1.01544,0.415981,0.889639,0.336106,0.236034,0.402028,0.436569,0.0880431,0.576478,0.387783,1.21515,0.730467,0.202389,0.574247,1.02557,0.547818,0.530785,0.92701,0.302275,0.225641,0.35719,0.577216,0.35388,0.585658,0.878269,1.28576,0.355745,0.513952,0.323162,0.390088,0.354447,0.468392,0.66382,0.542147,0.0909286,0.396429,0.745008,0.675919,0.891214,1.00488,1.15929,0.653901,0.400834,0.62023,1.65059,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.45007,1.15727,0.624519,0.594475,0.192925,0.84426,0.913168,0.477584,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,0.126687,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.30974,1.02023,0.32338,1.23175,0.987239,0.776336,1.53398,1.58445,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,1.21459,0.376529,1.13818,0.978783,1.10061,0.563054,1.29401,0.352243,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.520084,0.524606,1.40818,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.258882,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,2.2186,0.661335,0.0115686
}}
}}

Revision as of 14:50, 26 November 2012


Full id: C1351_immature_CD14_CD34_Peripheral_Mast_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr11:75048593..75048598,+p@chr11:75048593..75048598
+
Hg19::chr12:50099534..50099545,+p@chr12:50099534..50099545
+
Hg19::chr2:98279494..98279517,+p@chr2:98279494..98279517
+
Hg19::chr2:98279571..98279582,+p@chr2:98279571..98279582
+
Hg19::chr3:71113296..71113307,+p@chr3:71113296..71113307
+
Hg19::chr6:138114040..138114043,+p@chr6:138114040..138114043
+


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
leukocyte3.59e-41136
classical monocyte2.93e-3842
CD14-positive, CD16-negative classical monocyte2.93e-3842
granulocyte monocyte progenitor cell2.77e-3667
hematopoietic lineage restricted progenitor cell2.21e-35120
myeloid leukocyte6.19e-3572
hematopoietic cell8.21e-35177
defensive cell9.86e-3548
phagocyte9.86e-3548
nongranular leukocyte1.44e-33115
macrophage dendritic cell progenitor1.98e-3361
hematopoietic stem cell5.34e-33168
angioblastic mesenchymal cell5.34e-33168
myeloid lineage restricted progenitor cell3.53e-3266
hematopoietic oligopotent progenitor cell1.24e-30161
hematopoietic multipotent progenitor cell1.24e-30161
monopoietic cell5.46e-3059
monocyte5.46e-3059
monoblast5.46e-3059
promonocyte5.46e-3059
myeloid cell5.09e-27108
common myeloid progenitor5.09e-27108
stuff accumulating cell1.60e-1687
circulating cell1.32e-136
stem cell5.90e-13441
mesenchymal cell6.00e-13354
multi fate stem cell1.63e-12427
connective tissue cell2.26e-12361
somatic stem cell4.36e-12433
motile cell2.32e-10386
basophil9.28e-083
single nucleate cell1.17e-073
mononuclear cell1.17e-073
natural killer cell1.33e-073
pro-NK cell1.33e-073
somatic cell2.87e-07588
T cell7.05e-0725
pro-T cell7.05e-0725
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.73e-3198
blood island2.73e-3198
bone marrow9.52e-3176
hemolymphoid system9.55e-29108
bone element9.83e-2882
immune system1.13e-2493
skeletal element2.41e-2490
skeletal system7.02e-21100
connective tissue7.13e-13371
lateral plate mesoderm1.01e-12203
musculoskeletal system8.98e-11167
mesoderm7.58e-07315
mesoderm-derived structure7.58e-07315
presumptive mesoderm7.58e-07315


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
BATF#10538312.17890089615180.00125981487125340.00846133796391212
EBF1#187945.937644564379340.001975153636421710.0114888928228486
FOS#235345.998636872596270.001899823711886350.0111827587581411
FOSL1#8061213.23785990545770.00888833088009090.0337191568756198
GATA1#262336.780154071900220.006765763983348560.0287473403033743
GATA2#262448.496621155702660.0004993024497617180.00440911884253522
JUN#372536.256414596168170.008486346850954870.032407238976448
MEF2A#420539.371615454822030.002687399947103910.0147985533626271
NFKB1#479043.658708949462560.01207927289015230.0438235030178419
SPI1#668845.469549005681820.00269730053614140.014840552665371



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.