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Difference between revisions of "Coexpression cluster:C3053"

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|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296084095747454!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658250686855356!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323494233665374!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435242475172324!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459967665161957!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759724348023499!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089466016422402!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108275752508615!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887449714329355!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185676120820088!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00717983904428403!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029317096517762!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00198983874941111!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024491152201759!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469315163958541!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172231649320005!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268063307895912!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245395217446027!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203069847885504!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189474199352463!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327848408182333!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387573335340209!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108928255865369
 
|tf_chipseq_enrich=BRCA1#672;2:13.4561537621492:0.00711980771608456:0.0296084095747454!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00658250686855356!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323494233665374!E2F4#1874;3:12.6680603152844:0.000491798700629898:0.00435242475172324!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0459967665161957!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00759724348023499!FOS#2353;3:8.9979553088944:0.00137249927241713:0.0089466016422402!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0108275752508615!IRF3#3661;2:31.3213014743264:0.00133951467332011:0.00887449714329355!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185676120820088!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00717983904428403!MYC#4609;3:5.2222818716094:0.00702084375574015:0.029317096517762!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.00198983874941111!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.0024491152201759!NRF1#4899;3:12.2102794477109:0.000549217240102001:0.00469315163958541!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172231649320005!PBX3#5090;2:14.6096751244961:0.00605612247321789:0.0268063307895912!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245395217446027!SP2#6668;2:17.4356869958964:0.00427356848176974:0.0203069847885504!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189474199352463!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0327848408182333!ZNF143#7702;3:13.5008765522279:0.000406280496299717:0.00387573335340209!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0108928255865369
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.699513,0.869629,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,0.820209,0.985163,1.11328,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.824321,0.69094,0.242883,1.96998,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,0.427404,1.45286,1.99037,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.901413,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.92922,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,1.55552,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,1.54991,0.560075,0.450952,1.27663,1.05794,0.946807,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,2.36218,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.974093,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,2.04753,1.08214,2.31409,0.773313,0.539692,0.318511,1.99724,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,2.84192,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.951408
 
}}
 
}}

Revision as of 06:54, 26 November 2012


Full id: C3053_Eosinophils_Neutrophils_CD14_granulocyte_immature_CD8_Basophils



Phase1 CAGE Peaks

  Short description
Hg19::chr10:88281494..88281570,- p1@WAPAL
Hg19::chr16:75498553..75498621,- p1@TMEM170A
Hg19::chr5:139781445..139781487,+ p2@ANKHD1-EIF4EBP3
p2@ANKHD1


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 termp-valuen
hematopoietic stem cell6.03e-53168
angioblastic mesenchymal cell6.03e-53168
leukocyte4.66e-51136
hematopoietic oligopotent progenitor cell1.36e-49161
hematopoietic multipotent progenitor cell1.36e-49161
hematopoietic cell2.13e-48177
hematopoietic lineage restricted progenitor cell3.07e-42120
nongranular leukocyte9.80e-41115
myeloid cell1.39e-35108
common myeloid progenitor1.39e-35108
myeloid leukocyte1.14e-3472
granulocyte monocyte progenitor cell6.91e-3167
myeloid lineage restricted progenitor cell1.33e-2966
macrophage dendritic cell progenitor3.21e-2861
monopoietic cell2.56e-2759
monocyte2.56e-2759
monoblast2.56e-2759
promonocyte2.56e-2759
classical monocyte1.83e-2542
CD14-positive, CD16-negative classical monocyte1.83e-2542
defensive cell2.16e-2548
phagocyte2.16e-2548
nucleate cell1.35e-1255
lymphocyte2.76e-1253
common lymphoid progenitor2.76e-1253
lymphoid lineage restricted progenitor cell5.13e-1252
stuff accumulating cell1.04e-0887
lymphocyte of B lineage6.42e-0724
pro-B cell6.42e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.18e-3098
blood island1.18e-3098
hemolymphoid system1.11e-27108
bone element1.45e-2382
bone marrow5.55e-2376
immune system2.69e-2293
skeletal element3.38e-1890
skeletal system2.29e-14100


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#promotersEnrichmentp-valueq-value
BRCA1#672213.45615376214920.007119807716084560.0296084095747454
CHD2#1106310.34402283411690.0009033701102746880.00658250686855356
E2F1#186934.907389214879320.008460985347239390.0323494233665374
E2F4#1874312.66806031528440.0004917987006298980.00435242475172324
ELF1#199734.258097958807540.01295179875054610.0459967665161957
ETS1#211339.728760922202340.001085840092584840.00759724348023499
FOS#235338.99795530889440.001372499272417130.0089466016422402
HMGN3#932438.178547723350590.001827766942164210.0108275752508615
IRF3#3661231.32130147432640.001339514673320110.00887449714329355
MAX#414936.452555509007120.003721913834265510.0185676120820088
MXI1#460139.96157162875930.001011470541259020.00717983904428403
MYC#460935.22228187160940.007020843755740150.029317096517762
NFYA#4800318.42558069983050.0001598135507814160.00198983874941111
NFYB#4801316.75979325353650.0002123649923296180.0024491152201759
NRF1#4899312.21027944771090.0005492172401020010.00469315163958541
PAX5#507936.669565531177830.003370290999677260.0172231649320005
PBX3#5090214.60967512449610.006056122473217890.0268063307895912
SP1#666735.69838137814090.005403962701712170.0245395217446027
SP2#6668217.43568699589640.004273568481769740.0203069847885504
USF1#739136.361499277207960.00388404057290560.0189474199352463
YY1#752834.911170749853860.008441455341808260.0327848408182333
ZNF143#7702313.50087655222790.0004062804962997170.00387573335340209
ZNF263#1012738.221841637010680.001799043925565870.0108928255865369



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.