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Coexpression cluster:C2877: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;1.66718,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.100363,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;1.6149,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;1.1497,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;1.75269,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.0247757,MA0138.2;0.928035,MA0002.2;5.77536,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;1.99204,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:58, 22 January 2013


Full id: C2877_CD14_Eosinophils_neuroectodermal_CD8_cord_CD4_Natural



Phase1 CAGE Peaks

Hg19::chr7:130645970..130645981,-p@chr7:130645970..130645981
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Hg19::chr7:130645982..130645997,-p@chr7:130645982..130645997
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Hg19::chr7:130645999..130646023,-p@chr7:130645999..130646023
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Hg19::chr7:130646084..130646098,-p@chr7:130646084..130646098
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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
leukocyte6.88e-34136
nongranular leukocyte2.58e-30115
hematopoietic stem cell1.95e-28168
angioblastic mesenchymal cell1.95e-28168
hematopoietic cell3.70e-28177
hematopoietic oligopotent progenitor cell3.03e-27161
hematopoietic multipotent progenitor cell3.03e-27161
hematopoietic lineage restricted progenitor cell4.43e-24120
classical monocyte1.06e-1942
CD14-positive, CD16-negative classical monocyte1.06e-1942
defensive cell3.34e-1648
phagocyte3.34e-1648
mesenchymal cell1.20e-15354
lymphocyte1.69e-1553
common lymphoid progenitor1.69e-1553
motile cell2.83e-15386
lymphoid lineage restricted progenitor cell3.48e-1552
myeloid leukocyte5.28e-1572
nucleate cell3.27e-1455
connective tissue cell3.85e-14361
monopoietic cell2.67e-1359
monocyte2.67e-1359
monoblast2.67e-1359
promonocyte2.67e-1359
macrophage dendritic cell progenitor3.78e-1361
myeloid cell1.65e-12108
common myeloid progenitor1.65e-12108
T cell4.14e-1125
pro-T cell4.14e-1125
granulocyte monocyte progenitor cell2.70e-1067
myeloid lineage restricted progenitor cell6.04e-1066
mature alpha-beta T cell7.96e-1018
alpha-beta T cell7.96e-1018
immature T cell7.96e-1018
mature T cell7.96e-1018
immature alpha-beta T cell7.96e-1018
native cell2.30e-09722
multi fate stem cell3.70e-09427
somatic stem cell4.39e-09433
stem cell1.25e-08441
granulocyte5.79e-078
animal cell7.43e-07679
eukaryotic cell7.43e-07679
Uber Anatomy
Ontology termp-valuen
connective tissue2.54e-15371
hematopoietic system2.97e-1298
blood island2.97e-1298
bone element3.07e-1182
bone marrow2.12e-1076
skeletal element2.44e-1090
skeletal system3.05e-10100
hemolymphoid system1.93e-09108
immune system8.41e-0993


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.12.26728
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.11.66718
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.11.75269
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.0247757
MA0138.20.928035
MA0002.25.77536
MA0137.20.558189
MA0104.20.392359
MA0047.21.99204
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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#10538424.35780179230362.83869198020713e-069.79419067462348e-05
BCL11A#53335428.36945510360711.542446414682e-065.90728130190589e-05
BCL3#602434.54710280373837.01262157705428e-073.15413946979316e-05
BCLAF1#9774421.65264761012184.54636978835329e-060.000141863852502489
EBF1#187948.9064668465690.00015887907472010.00200038236102381
EP300#203346.77394172622320.0004748459821442640.0043525047857789
IRF4#3662421.91451268674414.33289161192893e-060.000136672566311763
JUND#372746.994663941871030.000417684217818580.00392606624289035
MAX#414946.452555509007120.0005767613195645490.00486483406994039
MEF2A#4205418.74323090964418.0978922767748e-060.000224690693808205
MEF2C#4208441.31135449262413.42889182145094e-071.70042750684005e-05
NFKB1#479045.488063424193840.001102199566301980.00769212298730453
PAX5#507946.669565531177830.0005052774169483260.00444909098294125
PBX3#5090421.91451268674414.33289161192893e-060.000136713857117295
POU2F2#545249.106124057742520.000145395665174930.00188773966623626
SIN3A#2594245.408884726815140.001168172384885160.00798081740727552
SRF#6722413.79717826216782.75840773062708e-050.000585658355314009
TAF1#687243.343046285745290.008005664898701650.0323306769403929
TBP#690843.706770687096390.005296377814784350.0245005272001711
TCF12#6938410.63446490218647.8163066689251e-050.00120278068689534
YY1#752844.911170749853860.00171871838055440.0107081804537804



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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