Coexpression cluster:C4411: Difference between revisions

Revision as of 16:43, 26 November 2012

Full id: C4411_pancreatic_salivary_CD14_parotid_submaxillary_choriocarcinoma_seminal

Phase1 CAGE Peaks

Hg19::chr4:40631779..40631790,-	p9@RBM47
Hg19::chr4:40631838..40631856,-	p3@RBM47
Hg19::chr4:40631859..40631889,-	p2@RBM47

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 disease_data

Cell Type
Ontology term	p-value	n
myeloid leukocyte	3.42e-30	72
macrophage dendritic cell progenitor	9.77e-28	61
granulocyte monocyte progenitor cell	1.62e-27	67
monopoietic cell	1.27e-26	59
monocyte	1.27e-26	59
monoblast	1.27e-26	59
promonocyte	1.27e-26	59
defensive cell	6.35e-26	48
phagocyte	6.35e-26	48
myeloid lineage restricted progenitor cell	9.85e-25	66
classical monocyte	1.68e-22	42
CD14-positive, CD16-negative classical monocyte	1.68e-22	42
myeloid cell	4.60e-14	108
common myeloid progenitor	4.60e-14	108
stuff accumulating cell	3.34e-12	87
leukocyte	2.08e-11	136
hematopoietic lineage restricted progenitor cell	7.30e-08	120
nongranular leukocyte	9.84e-08	115

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	5.84e-24	98
blood island	5.84e-24	98
bone marrow	1.12e-22	76
bone element	9.40e-22	82
hemolymphoid system	7.13e-20	108
skeletal element	6.60e-19	90
immune system	6.51e-18	93
organ	2.39e-16	503
skeletal system	1.56e-14	100
embryo	1.82e-09	592
multi-cellular organism	3.31e-09	656
developing anatomical structure	4.75e-09	581
anatomical system	1.38e-08	624
anatomical group	2.21e-08	625
endoderm-derived structure	5.04e-08	160
endoderm	5.04e-08	160
presumptive endoderm	5.04e-08	160
immaterial anatomical entity	7.99e-08	117
digestive system	1.59e-07	145
digestive tract	1.59e-07	145
primitive gut	1.59e-07	145
anatomical space	1.82e-07	95
subdivision of digestive tract	2.01e-07	118
embryonic structure	3.69e-07	564

Disease
Ontology term	p-value	n
carcinoma	9.73e-08	106

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	#promoters	Enrichment	p-value	q-value
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0280693452767203
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0326904978979814
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.000853314076697315
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.0043528477885661
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309752969170198
NRF1#4899	3	12.2102794477109	0.000549217240102001	0.00472718801211578
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173453812504457
STAT1#6772	3	20.7065874971992	0.000112599244104667	0.00155203279068857
STAT3#6774	3	10.5194649971542	0.000858918453041531	0.00644707376147797
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00617903815578119
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190927851545556
USF2#7392	3	12.9921973850696	0.000455897939342781	0.00422555243938771

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.

@@ Line 8: / Line 8: @@
 |tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0280693452767203!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326904978979814!GATA3#2625;3:27.236516357206:4.94721007899563e-05:0.000853314076697315!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.0043528477885661!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309752969170198!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00472718801211578!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0173453812504457!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155203279068857!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00644707376147797!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00617903815578119!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0190927851545556!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00422555243938771
 |tfbs_overrepresentation=0.147255,0.0586687,0.039404,0.0477154,0.199763,0.287811,0.0430074,0.414564,0.03272,0.0257057,0.0102054,0.000144577,0.188771,1.23007e-05,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.0190294,0.132577,9.78244e-05,0.0948982,0.0415721,0.215492,0.00181435,0.0907212,0.143747,0.0933697,0.0226057,0.00676561,0.0180314,4.76405e-06,0.0665252,0.0844722,0.324808,0.0429682,0.120351,0.0667043,0.00481151,0.0246116,0.140039,0.184019,0.120917,0.0362416,0.0380166,0.18151,0.000250563,0.121201,0.154071,0.00149495,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,2.81024e-08,0.105572,3.2394e-08,0.000625972,0.108602,0.0759481,0.054569,0.0504887,0.0709764,0.00183766,0.0860723,0.167053,0.000137668,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.000156996,0.226912,0.0425,8.37227e-06,0.0472875,0.0347684,0.064341,0.209032,0.000428223,0.062747,6.68145e-10,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,3.75188e-05,0.153631,3.45987e-06,0.27413,0.0574857,0.0422457,0.141874,8.73035e-06,0.219088,0.0409286,0.0669887,0.00087036,0.0109386,0.0400492,0.182599,0.0339971,2.52137e-05,0.0176855,0.005305,0.000576135,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.0857827,0.102368,0.00106363,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,6.16389e-06,0.00395526,0.022776,0.127606,0.0223702,0.155998,0.0641358,0.0693171,0.0988228,0.00365114,0.0389418,0.120833,0.0216297,0.0108547,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.0283286,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,9.1684e-10,0.127369,0.0403542,0.312091,0.179689,0.00995227,0.46397,0.0541353,0.0799324,0.000130634,0.140334,5.75739e-05,6.77036e-08,0.0356339,0.000758098,0.122474,0.0274061,0.115574,0.0737247,0.000307105,0.00118409,0.0401756,0.0828697,0.173562,0.107145,6.5333e-05,0.122935,0.0284396,0.112671,0.0470731,0.0782523,0.0602859,0.0676496,0.109673,0.0893019,0.00186183,0.0308319,6.05487e-07,0.136451,0.037005,0.000337223,0.15185,0.206299,0.0169462,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.0142864,0.100942,0.062995,0.10299,0.0105855,0.37245,0.15606,0.161026,0.0738599,0.00837667,0.138852,0.085973,0.060453,0.059896,0.569726,0.0859236,0.0418404,2.49041e-08,0.0959204,0.0931946,0.0472272,0.00377835,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.00703932,0.136838,0.0034161,0.111647,9.61262e-06,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.00022351,0.00161471,0.0695832,0.0585224,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,9.48809e-05,0.0043744,0.118078,0.0755168,0.278352,7.22729e-07,0.254773,0.119261,0.0865903,0.0380459,0.00886625,0.059488,0.0381789,0.198118,0.635872,0.563047,0.000443992,1.3468e-06,0.00083951,0.629514,0.261553,0.446302,0.373681,0.000581634,0.147559,0.330703,0.000178425,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.0148713,0.581713,0.000362379,0.187251,0.362792,0.0176124,0.10624,0.109988,0.0620388,0.218329,0.0190732,0.376924,0.129235,0.0217334,0.0407001,0.520763,0.370782,0.101703,0.142924,0.00335333,0.276829,0.301787,0.481778,0.316882,0.223503,0.503224,0.0669244,0.0447111,0.314747,0.000273712,0.00529148,0.120054,0.576651,0.416816,0.0478086,5.90455e-05,0.439556,0.373868,0.57762,0.0154652,0.18237,0.126021,0.821217,0.400457,0.275351,0.236471,0.185661,0.0684159,0.0427964,0.270984,0.000544819,0.00573308,0.000896465,0.169228,0.00314692,0.281576,0.135034,3.64678e-05,0.0670502,0.0730934,0.184794,0.000359684,0.0582356,0.581837,0.0169683,0.671377,0.546839,0.191921,0.448039,6.20339e-06,0.000612438,0.00743804,0.0451077,0.00286634,0.229003,0.00449125,0.00223439,0.154921,0.0484563,0.34331,0.138202,7.95672e-08,3.82836e-06,0.319027,0.00452305,0.0263998,0.428671,0.000152311,0.00847033,0.19763,0.000720848,0.0530502,0.104858,0.141711,0.420626,0.516462,0.858756,0.335105,0.144809,0.0005766,5.09402e-08,0.376191,0.0224279,0.127215,0.252232,0.152681,0.0465712,0.00985947,0.00360191,0.134788,0.000172424,0.546222,0.293698,0.284593,0.0673219,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.0965765,0.102469,0.0760312,0.464871,0.00320894,0.206222,0.171685,0.000779217,0.113671,0.269226,0.339277,0.0479524,0.0439467,0.141758,0.124432,0.168058,0.0134764,0.238587,0.0799758,0.232251,9.98681e-08,0.0891382,0.0595618,0.0397695,0.0178839,0.0688327,0.539392,0.34988,0.475069,0.0158269,0.6408,0.262389,0.316179,0.0697683,0.0556835,0.192544,8.39939e-05,0.0575676,2.17134e-05,0.223391,0.0223093,0.0216577,0.441735,0.191777,0.111931,0.28934,0.0435386,0.00601662,0.00835866,0.134852,0.10689,0.00427764,0.0627924,0.381386,0.0179103,0.303939,0.0434097,0.00016427,0.0464827,0.169603,0.114583,0.00566743,0.0899537,0.0866966,0.15983,0.107111,1.45442e-05,0.00389058,0.123593,0.129156,0.210369,0.193675,0.0684384,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.00817962,0.00146083,0.132201,0.188694,0.0481795,0.0214786,0.016022,0.00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+|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,1.65103,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,1.18351,0.820209,0.985163,0.436625,0.925331,1.54465,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.137917,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,1.54087,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,2.8077,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,2.41357,1.45054,3.91579,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,1.76229,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.99742,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,7.81842,0.794219,1.10778,2.3166,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,1.29196,1.37083,0.481626,2.16614,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,2.15653,0.0768232
 }}

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Coexpression cluster:C4411: Difference between revisions

From FANTOM5_SSTAR

Revision as of 16:43, 26 November 2012

Phase1 CAGE Peaks

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