Coexpression cluster:C2621: Difference between revisions

Revision as of 15:37, 26 November 2012

Full id: C2621_migratory_Eosinophils_Neutrophils_CD14_hairy_immature_Mast

Phase1 CAGE Peaks

Hg19::chr20:4803297..4803323,-	p@chr20:4803297..4803323 -
Hg19::chr22:35806477..35806519,+	p3@MCM5
Hg19::chr22:35806599..35806615,+	p8@MCM5
Hg19::chr6:12061235..12061270,+	p@chr6:12061235..12061270 +

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

Cell Type
Ontology term	p-value	n
leukocyte	1.70e-82	136
nongranular leukocyte	6.02e-69	115
hematopoietic stem cell	1.57e-63	168
angioblastic mesenchymal cell	1.57e-63	168
hematopoietic lineage restricted progenitor cell	1.67e-62	120
hematopoietic cell	8.02e-62	177
hematopoietic oligopotent progenitor cell	7.11e-59	161
hematopoietic multipotent progenitor cell	7.11e-59	161
myeloid leukocyte	1.83e-46	72
macrophage dendritic cell progenitor	1.73e-43	61
defensive cell	1.22e-42	48
phagocyte	1.22e-42	48
classical monocyte	1.58e-42	42
CD14-positive, CD16-negative classical monocyte	1.58e-42	42
monopoietic cell	2.31e-41	59
monocyte	2.31e-41	59
monoblast	2.31e-41	59
promonocyte	2.31e-41	59
granulocyte monocyte progenitor cell	6.37e-39	67
myeloid lineage restricted progenitor cell	5.21e-36	66
myeloid cell	8.40e-33	108
common myeloid progenitor	8.40e-33	108
lymphocyte	2.99e-23	53
common lymphoid progenitor	2.99e-23	53
lymphoid lineage restricted progenitor cell	1.82e-22	52
nucleate cell	7.33e-22	55
lymphocyte of B lineage	2.23e-19	24
pro-B cell	2.23e-19	24
stuff accumulating cell	1.52e-15	87
dendritic cell	9.35e-12	10
B cell	1.74e-10	14
mesenchymal cell	1.86e-10	354
intermediate monocyte	2.45e-10	9
CD14-positive, CD16-positive monocyte	2.45e-10	9
granulocyte	2.84e-10	8
conventional dendritic cell	5.92e-10	8
connective tissue cell	1.14e-09	361
blood cell	3.66e-08	11
Langerhans cell	3.33e-07	5
motile cell	5.06e-07	386

Uber Anatomy
Ontology term	p-value	n
hematopoietic system	5.61e-47	98
blood island	5.61e-47	98
hemolymphoid system	6.33e-43	108
bone marrow	1.23e-34	76
immune system	1.73e-34	93
bone element	1.61e-30	82
skeletal element	6.29e-26	90
skeletal system	4.38e-22	100
adult organism	2.28e-16	114
neural tube	3.14e-13	56
neural rod	3.14e-13	56
future spinal cord	3.14e-13	56
neural keel	3.14e-13	56
regional part of nervous system	1.34e-12	53
regional part of brain	1.34e-12	53
lateral plate mesoderm	1.48e-11	203
brain grey matter	7.72e-11	34
gray matter	7.72e-11	34
telencephalon	1.03e-10	34
regional part of forebrain	2.73e-10	41
forebrain	2.73e-10	41
anterior neural tube	2.73e-10	41
future forebrain	2.73e-10	41
regional part of telencephalon	1.03e-09	32
cerebral hemisphere	1.23e-09	32
blood	4.73e-09	15
haemolymphatic fluid	4.73e-09	15
organism substance	4.73e-09	15
regional part of cerebral cortex	5.94e-09	22
connective tissue	6.34e-09	371
brain	4.01e-08	68
future brain	4.01e-08	68
neocortex	7.23e-08	20
central nervous system	1.86e-07	81
cerebral cortex	2.39e-07	25
pallium	2.39e-07	25
neural plate	7.08e-07	82
presumptive neural plate	7.08e-07	82

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
BATF#10538	2	12.1789008961518	0.00956675880504781	0.0360233170911591
EBF1#1879	3	6.67985013492675	0.00518429411827891	0.024052351891028
IRF4#3662	3	16.4358845150581	0.000366943139555461	0.00365888624709116
MAX#4149	3	4.83941663175534	0.0131573713783684	0.046634857441981
NFKB1#4790	4	5.48806342419384	0.00110219956630198	0.00768390765002418
PAX5#5079	4	6.66956553117783	0.000505277416948326	0.00444234936852144
PBX3#5090	2	10.9572563433721	0.0117453018068803	0.0428545128356895
SPI1#6688	3	6.15324263139204	0.00658038711305903	0.0281048971373971
TCF12#6938	3	7.97584867663982	0.00309092039601307	0.0162822876646428
USF1#7391	3	4.77112445790597	0.0137046588718802	0.0483123225518225

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=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360233170911591!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.024052351891028!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365888624709116!MAX#4149;3:4.83941663175534:0.0131573713783684:0.046634857441981!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768390765002418!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444234936852144!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428545128356895!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281048971373971!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162822876646428!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483123225518225
 |tfbs_overrepresentation=0.191353,0.0774498,0.50138,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.0423226,0.268949,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.788552,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,0.113084,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.0780785,0.320801,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.327332,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.122756,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.675167,0.476758,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.324438,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.545829,0.113754,0.0504034,0.169684,0.327364,0.233666,0.603871,0.73998,0.668426,0.407767,0.644298,0.420045,0.73391,0.332539,0.545329,0.464128,0.389374,0.594055,0.414547,0.489273,0.413223,0.639461,0.364388,0.34505,0.369161,0.500422,0.49089,0.323639,0.341822,0.241524,0.45167,0.234628,0.168228,0.143893,0.101233,0.0434592,0.170724,0.467825,0.563725,0.751064,0.632838,0.624969,0.460819,0.511459,0.586668,0.322903,0.0703732,0.380582,0.583749,0.0926754,0.286293,0.606558,0.34907,0.359128,0.395864,0.683133,0.368633,0.547291,0.682118,0.512763,0.0789041,0.578349,0.537928,0.0255795,0.109673,0.714007,0.235444,0.48585,0.402752,0.279301,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.377117,0.606382,0.0733855,0.626346,0.316925,0.0728506,0.210197,0.211506,0.0883859,0.0962508,0.238465,0.0346954,0.853221,0.112487,0.159267,0.773224,0.651927,0.656755,0.54723,0.280307,0.393583,0.469888,0.0596868,0.0984075,0.0478748,0.408321,0.332526,0.605423,0.372182,0.429205,0.578951,0.365653,0.41035,0.784024,0.35234,0.376421,0.525923,0.291917,0.421082,0.25441,0.202782,0.307342,0.517933,0.584705,0.517001,0.620475,0.926442,0.103882,0.188259,0.189182,0.477589,0.46699,0.187849,0.560187,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.360161,0.429696,0.386216,0.385297,0.706685,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.153861,0.513045,0.452694,0.565545,0.287542,0.265037,0.629795,0.410093,0.179179,0.341771,0.424526,0.657528,0.356381,0.184395,0.55524,0.256884,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.0789416,0.729876,0.433821,0.64428,0.436806,0.576549,0.499072,0.158149,0.382579,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.540322,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,0.0828344,0.135364,0.0238089,0.383126,0.354433,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.00674695,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.111145,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.099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+|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,1.02453,1.01802,0.151681,1.68405,0.867962,0.341754,0.809319,1.31925,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.975621,0.731221,0.528529,0.632849,0.892087,0.316693,0.728867,0.537869,0.806311,0.682839,1.09415,0.433165,0.344471,0.49475,0.285913,0.491074,0.740899,1.17228,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,0.61613,0.822818,0.694903,0.99221,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.692875,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.716653,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,2.02143,1.24863,0.68598,1.37788,0.852645,1.52813,0.774456,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,2.22181,0.632914,1.4628,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,0.156682
 }}

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Coexpression cluster:C2621: Difference between revisions

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Revision as of 15:37, 26 November 2012

Phase1 CAGE Peaks

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