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Coexpression cluster:C2154: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,2.74508,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,3.55418,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,1.53358,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,2.14358,1.00622,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,2.53981,0.822818,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,1.72726,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,1.17564,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,1.64086,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.95303,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,3.03252
|tfbs_overrepresentation_for_novel_motifs=0.590005,2.74508,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,3.55418,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,1.53358,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,2.14358,1.00622,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.539378,0.53106,1.08066,2.53981,0.822818,1.65941,0.173425,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.893276,0.321165,0.305238,1.00941,1.08,0.62601,0.95118,1.02594,0.844168,0.399165,1.27559,1.72726,0.6318,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.354969,1.15558,0.939507,0.749003,1.17564,1.1057,1.14983,1.05974,0.979006,1.67377,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.27972,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,1.64086,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,1.95303,0.234974,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.08488,0.820225,3.03252
|tfbs_overrepresentation_jaspar=MA0003.1;5.41581,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.896009,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.946082,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;2.31526,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;1.18043,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;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;0.656404,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;1.13665,MA0115.1;1.45393,MA0116.1;1.15856,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;0.912459,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;2.31379,MA0147.1;2.03364,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;1.5472,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;2.43626,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;2.15942,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;2.00408,MA0102.2;1.75932,MA0258.1;1.07498,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:27, 22 January 2013


Full id: C2154_Eosinophils_Neutrophils_Renal_Endothelial_tridermal_Hepatic_Basophils



Phase1 CAGE Peaks

Hg19::chr11:65381643..65381767,-p1@MAP3K11
Hg19::chr22:22307182..22307197,-p2@PPM1F
Hg19::chr22:22307199..22307242,-p1@PPM1F
Hg19::chr3:50273625..50273655,+p1@GNAI2


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

GO IDGO nameFDR corrected p-value
GO:0004706JUN kinase kinase kinase activity0.0259929336955715
GO:0050790regulation of catalytic activity0.0259929336955715
GO:0065009regulation of a molecular function0.0259929336955715
GO:0031280negative regulation of cyclase activity0.0259929336955715
GO:0007194negative regulation of adenylate cyclase activity0.0259929336955715
GO:0051350negative regulation of lyase activity0.0259929336955715
GO:0000080G1 phase of mitotic cell cycle0.0259929336955715
GO:0004709MAP kinase kinase kinase activity0.0259929336955715
GO:0046328regulation of JNK cascade0.0259929336955715
GO:0051318G1 phase0.0259929336955715
GO:0007257activation of JNK activity0.0261157639195323
GO:0043507positive regulation of JNK activity0.0262178539814203
GO:0043506regulation of JNK activity0.0263039900870814
GO:0015071protein phosphatase type 2C activity0.0314401238840169
GO:0045761regulation of adenylate cyclase activity0.0314401238840169
GO:0007584response to nutrient0.0314401238840169
GO:0031279regulation of cyclase activity0.0314401238840169
GO:0051339regulation of lyase activity0.0314401238840169
GO:0046777protein amino acid autophosphorylation0.0314401238840169
GO:0016540protein autoprocessing0.0314401238840169
GO:0000187activation of MAPK activity0.0320321372125483
GO:0008287protein serine/threonine phosphatase complex0.0320321372125483
GO:0031667response to nutrient levels0.0320321372125483
GO:0051259protein oligomerization0.0320321372125483
GO:0007254JNK cascade0.0320321372125483
GO:0004722protein serine/threonine phosphatase activity0.0320321372125483
GO:0009991response to extracellular stimulus0.0320321372125483
GO:0043406positive regulation of MAP kinase activity0.0320321372125483
GO:0031098stress-activated protein kinase signaling pathway0.0320321372125483
GO:0004702receptor signaling protein serine/threonine kinase activity0.0329950406170268
GO:0006793phosphorus metabolic process0.0329950406170268
GO:0006796phosphate metabolic process0.0329950406170268
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.0329950406170268
GO:0051329interphase of mitotic cell cycle0.0329950406170268
GO:0019933cAMP-mediated signaling0.0329950406170268
GO:0043086negative regulation of catalytic activity0.0329950406170268
GO:0051325interphase0.0332073572743918
GO:0043405regulation of MAP kinase activity0.0334083090119861
GO:0016485protein processing0.0346456689926608
GO:0007242intracellular signaling cascade0.037377126989421
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.0389269169469197
GO:0019935cyclic-nucleotide-mediated signaling0.0396181824281736
GO:0005813centrosome0.0408833829227281
GO:0045860positive regulation of protein kinase activity0.0408833829227281
GO:0043687post-translational protein modification0.0408833829227281
GO:0033674positive regulation of kinase activity0.0408833829227281
GO:0030145manganese ion binding0.0408833829227281
GO:0005815microtubule organizing center0.0408833829227281
GO:0051347positive regulation of transferase activity0.0408833829227281
GO:0000165MAPKKK cascade0.0408833829227281
GO:0042803protein homodimerization activity0.0422094848719357
GO:0005057receptor signaling protein activity0.0463500026719706



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
myeloid leukocyte4.31e-2772
defensive cell1.09e-2448
phagocyte1.09e-2448
macrophage dendritic cell progenitor3.91e-2461
monopoietic cell1.66e-2359
monocyte1.66e-2359
monoblast1.66e-2359
promonocyte1.66e-2359
granulocyte monocyte progenitor cell1.78e-2367
classical monocyte1.84e-2342
CD14-positive, CD16-negative classical monocyte1.84e-2342
myeloid cell1.38e-22108
common myeloid progenitor1.38e-22108
endothelial cell8.13e-2136
myeloid lineage restricted progenitor cell4.90e-2066
meso-epithelial cell1.71e-1645
endothelial cell of vascular tree7.43e-1624
mesodermal cell3.98e-15121
somatic cell7.10e-13588
blood vessel endothelial cell8.19e-1318
embryonic blood vessel endothelial progenitor cell8.19e-1318
stuff accumulating cell1.13e-1187
lining cell2.75e-1058
barrier cell2.75e-1058
multi fate stem cell5.58e-09427
somatic stem cell1.41e-08433
hematopoietic cell2.37e-08177
hematopoietic stem cell5.39e-08168
angioblastic mesenchymal cell5.39e-08168
stem cell6.65e-08441
hematopoietic oligopotent progenitor cell1.44e-07161
hematopoietic multipotent progenitor cell1.44e-07161
leukocyte2.32e-07136
endothelial cell of artery3.74e-079
contractile cell6.00e-0759
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm1.87e-47203
mesoderm3.15e-30315
mesoderm-derived structure3.15e-30315
presumptive mesoderm3.15e-30315
hemolymphoid system4.38e-28108
circulatory system6.23e-26112
cardiovascular system1.63e-25109
immune system3.48e-2493
hematopoietic system3.50e-2498
blood island3.50e-2498
bone marrow8.28e-2276
vasculature1.45e-2178
vascular system1.45e-2178
vessel2.35e-2168
splanchnic layer of lateral plate mesoderm3.39e-1983
epithelial tube open at both ends1.57e-1859
blood vessel1.57e-1859
blood vasculature1.57e-1859
vascular cord1.57e-1859
musculoskeletal system2.04e-18167
bone element8.84e-1882
skeletal element9.34e-1590
epithelial tube1.19e-13117
skeletal system3.95e-13100
blood vessel endothelium8.19e-1318
endothelium8.19e-1318
cardiovascular system endothelium8.19e-1318
artery2.85e-1242
arterial blood vessel2.85e-1242
arterial system2.85e-1242
simple squamous epithelium2.14e-1022
anatomical system8.59e-10624
anatomical group1.57e-09625
systemic artery4.69e-0933
systemic arterial system4.69e-0933
germ layer9.68e-09560
germ layer / neural crest9.68e-09560
embryonic tissue9.68e-09560
presumptive structure9.68e-09560
germ layer / neural crest derived structure9.68e-09560
epiblast (generic)9.68e-09560
tissue1.16e-08773
embryonic structure1.93e-08564
epithelial vesicle3.52e-0878
squamous epithelium4.05e-0825
developing anatomical structure4.38e-08581
embryo5.42e-08592
endothelial tube3.74e-079
arterial system endothelium3.74e-079
endothelium of artery3.74e-079
multi-cellular organism5.37e-07656


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)
MA0003.15.41581
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.12.31526
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.11.18043
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.11.15856
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.12.31379
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.5472
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.22.43626
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.12.15942
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.22.00408
MA0102.21.75932
MA0258.11.07498
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
E2F1#186944.907389214879320.001724022357361790.0106271127297709
ELF1#199744.258097958807540.003041525565781240.0160577236156418
HEY1#2346244.040111043105710.00375304636917980.0185589209162296
JUNB#3726215.30531632991060.006126947148475620.0270934132119419
MAFK#7975320.32554985337240.0001953213688931110.00235040539760659
NFKB1#479045.488063424193840.001102199566301980.00766650819214201
PAX5#507946.669565531177830.0005052774169483260.00443153074812447
TAF1#687243.343046285745290.008005664898701650.0321306446989279
TBP#690843.706770687096390.005296377814784350.0243527517213288
TFAP2A#7020312.38897577978370.000846941303588430.00637917948979317
TFAP2C#702238.106921457395170.002947011739866440.0157152391677259



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2154&oldid=2570665"