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Coexpression cluster:C1047: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348717,0.183537,0.905112,0.481684,0.301904,0.480078,1.36559,0.561282,0.190005,0.994235,1.99636,0.597407,0.152895,1.34165,0.300614,0.322799,0.774423,0.250594,0.491486,0.560708,0.341703,2.63202,1.1906,0.29709,1.00212,2.55172,0.135503,0.470396,0.304828,1.26774,0.429397,0.810962,0.220667,0.469827,0.742281,0.339976,0.735464,0.481208,1.27056,2.25462,0.268162,1.06332,0.444349,0.299183,0.637759,1.72504,1.36786,1.12076,0.186577,0.822946,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.308962,0.514077,0.388089,0.513089,0.85167,1.37279,0.556977,1.76725,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,1.03556,0.573519,0.0911419,1.03748,0.149081,0.429044,1.88626,0.730167,0.797419,0.379656,0.167664,0.745864,0.575394,1.07768,0.986227,0.730725,0.0757344,1.24284,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.302606,0.239285,0.162291,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,1.67288,0.446229,0.762347,0.539961,1.00159,2.18389,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.826889,0.428232,0.710479,0.229841,1.02923,0.657218,1.20107,0.586509,1.28328,1.73413,0.548418,0.83262,1.07171,3.57806,0.960022,0.432175,1.08604,0.583225,1.23359,0.113443,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,0.593875,0.743411,0.960402,1.03091,0.557588,1.36372,0.643609,0.288769,0.385642,0.357927,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.213234,0.553354,2.80701
|tfbs_overrepresentation_jaspar=MA0003.1;0.797136,MA0004.1;0.455723,MA0006.1;0.812175,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;1.03236,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.653157,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;6.62303,MA0056.1;0,MA0057.1;0.305162,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;1.06021,MA0061.1;0.961853,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.415214,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.131075,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.770971,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.818737,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;2.64083,MA0106.1;1.45807,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.155155,MA0140.1;1.28413,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;2.31266,MA0146.1;3.51017,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.485915,MA0035.2;0.515566,MA0039.2;4.44385,MA0138.2;0.653421,MA0002.2;0.531206,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.458158,MA0065.2;0.490252,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;1.64163,MA0156.1;0.865715,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.682702,MA0160.1;0.495355,MA0161.1;0,MA0162.1;4.37832,MA0163.1;0.75401,MA0164.1;0.627336,MA0080.2;0.818924,MA0018.2;0.599912,MA0099.2;1.29876,MA0079.2;7.67909,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;1.29349,MA0442.1;0
}}
}}

Revision as of 19:39, 22 January 2013


Full id: C1047_Whole_blood_CD14_Neutrophils_Eosinophils_Reticulocytes_Mast



Phase1 CAGE Peaks

Hg19::chr17:21188012..21188031,+p1@MAP2K3
Hg19::chr17:21188043..21188069,+p2@MAP2K3
Hg19::chr17:21188075..21188079,+p4@MAP2K3
Hg19::chr4:2801321..2801334,+p@chr4:2801321..2801334
+
Hg19::chr6:108882109..108882173,+p2@FOXO3
Hg19::chr6:108882364..108882391,+p4@FOXO3
Hg19::chr7:35469..35507,-p1@ENST00000469418
Hg19::chrX:67718803..67718831,-p@chrX:67718803..67718831
-


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

p.valueFDRnGenesnPathwayName
2.92938943019595e-050.01013069629868642155TGF-beta Receptor Signaling Pathway (Wikipathways):WP366
3.20085191111734e-050.01013069629868642162Insulin Signaling (Wikipathways):WP481



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:0045893positive regulation of transcription, DNA-dependent0.002668471739994
GO:0045941positive regulation of transcription0.002668471739994
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.002668471739994
GO:0031325positive regulation of cellular metabolic process0.00293335680241988
GO:0009893positive regulation of metabolic process0.00293335680241988
GO:0045648positive regulation of erythrocyte differentiation0.00544534052623127
GO:0045646regulation of erythrocyte differentiation0.0079495422567252
GO:0004708MAP kinase kinase activity0.0079495422567252
GO:0004712protein serine/threonine/tyrosine kinase activity0.0079495422567252
GO:0045639positive regulation of myeloid cell differentiation0.0079495422567252
GO:0048522positive regulation of cellular process0.0079495422567252
GO:0048518positive regulation of biological process0.00903133988169789
GO:0030218erythrocyte differentiation0.0158625041483939
GO:0045637regulation of myeloid cell differentiation0.0158625041483939
GO:0045597positive regulation of cell differentiation0.0204618228353415
GO:0051094positive regulation of developmental process0.027745483969377
GO:0030099myeloid cell differentiation0.0295656607028872
GO:0019901protein kinase binding0.0300962908074367
GO:0019900kinase binding0.0340005992307244
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.0393274420359954
GO:0045860positive regulation of protein kinase activity0.0393274420359954
GO:0045595regulation of cell differentiation0.0393274420359954
GO:0033674positive regulation of kinase activity0.0393274420359954
GO:0051347positive regulation of transferase activity0.0393274420359954
GO:0030097hemopoiesis0.0393274420359954
GO:0006355regulation of transcription, DNA-dependent0.0393274420359954
GO:0048534hemopoietic or lymphoid organ development0.0393274420359954
GO:0006351transcription, DNA-dependent0.0393274420359954
GO:0032774RNA biosynthetic process0.0393274420359954
GO:0002520immune system development0.0395387988639219
GO:0045449regulation of transcription0.0396816272126048
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0396816272126048
GO:0006350transcription0.0396816272126048
GO:0010468regulation of gene expression0.0396816272126048
GO:0031323regulation of cellular metabolic process0.0396816272126048
GO:0050793regulation of developmental process0.0396816272126048
GO:0045859regulation of protein kinase activity0.0396816272126048
GO:0043549regulation of kinase activity0.0396816272126048
GO:0051338regulation of transferase activity0.0396816272126048
GO:0019222regulation of metabolic process0.0396816272126048
GO:0016070RNA metabolic process0.0396816272126048
GO:0043085positive regulation of catalytic activity0.0396816272126048
GO:0019899enzyme binding0.0446688293427135
GO:0004713protein-tyrosine kinase activity0.0446688293427135
GO:0016563transcription activator activity0.0446688293427135



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>

Uber Anatomy
Ontology termp-valuen
hematopoietic system2.45e-2198
blood island2.45e-2198
hemolymphoid system7.53e-20108
bone marrow1.67e-1976
bone element1.74e-1782
lateral plate mesoderm2.78e-17203
musculoskeletal system6.35e-16167
skeletal system7.40e-16100
immune system1.60e-1593
multi-cellular organism3.65e-15656
skeletal element6.39e-1590
mesoderm3.66e-14315
mesoderm-derived structure3.66e-14315
presumptive mesoderm3.66e-14315
anatomical system4.78e-14624
anatomical group5.77e-14625
germ layer4.83e-10560
germ layer / neural crest4.83e-10560
embryonic tissue4.83e-10560
presumptive structure4.83e-10560
germ layer / neural crest derived structure4.83e-10560
epiblast (generic)4.83e-10560
embryonic structure1.03e-09564
developing anatomical structure1.19e-09581
embryo1.69e-09592
adult organism5.63e-07114


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)
MA0003.10.797136
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.11.03236
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.16.62303
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.11.06021
MA0061.10.961853
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.131075
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.770971
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.818737
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.12.64083
MA0106.11.45807
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.11.28413
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.12.31266
MA0146.13.51017
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.485915
MA0035.20.515566
MA0039.24.44385
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.458158
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.11.64163
MA0156.10.865715
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.14.37832
MA0163.10.75401
MA0164.10.627336
MA0080.20.818924
MA0018.20.599912
MA0099.21.29876
MA0079.27.67909
MA0102.21.46209
MA0258.10.603127
MA0259.11.29349
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
CHD2#110656.465014271323040.0003676243258073190.00366078537023175
FOSL2#235536.348825226710630.009211946658641070.0348266605278485
HEY1#2346263.030083282329280.004001723466483270.0191854570839169
MAFK#7975310.16277492668620.002445573107139520.0137681639661767
NFYA#480036.909592762436450.007279727237130680.030122323015796
NFYB#480136.284922470076170.009473769012482620.0356963331371193
PBX3#509038.217942257529050.004473206582808440.0211670165512179
REST#597844.825014358064010.005720735398269540.0257873833251272
SIN3A#2594253.380552954259460.007342226961170280.0303652968596865
SP2#666839.807573935191740.002707184665085610.0148863085998461
TAF1#687262.507284714308970.01111734475613860.0408832524290973
TBP#690862.780078015322290.006390181121263010.0278030380821358



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:C1047&oldid=2569558"