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Coexpression cluster:C439: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.0942734,0.0205503,0.303044,1.0012,0.0703126,0.518467,0.226953,0.269959,0.26513,0.0446441,0.155105,0.717665,0.0724758,0.218743,0.0696927,0.580599,0.401017,0.17941,0.983198,0.25119,0.0905079,0.129045,0.169484,0.240266,0.115011,0.275879,0.799245,0.502604,0.250879,0.269248,0.141557,0.432083,0.0360115,0.191773,0.448262,0.133108,0.0541423,0.175318,0.690898,0.231945,0.445121,0.411741,0.428928,0.243124,0.0543932,0.106689,0.64558,0.453623,0.136995,0.535654,0.286755,0.665516,0.324106,0.49846,0.635443,0.629339,0.256602,0.197918,0.130563,0.573275,0.467239,0.22944,0.796223,0.377975,0.680025,0.923233,0.716956,1.06805,1.08432,0.911622,0.391938,0.830452,0.00448968,0.633615,0.0147578,0.0598881,0.13996,0.364079,1.07834,0.35946,1.39193,0.377089,0.679423,1.1868,0.586887,0.0386897,0.0562057,0.257083,0.306981,1.1648,0.804514,0.562601,1.13448,0.150965,0.247818,0.376385,0.974895,0.483243,0.310601,0.21846,0.173754,0.441596,0.47839,1.04259,0.902569,0.15226,0.39086,0.216299,0.114869,0.0632414,0.31873,0.475985,0.615165,0.161084,0.759328,0.764885,0.00180706,0.434767,0.347912,1.41471,0.626054,0.305079,0.172748,0.25053,0.863933,0.364702,0.222409,0.450719,0.66511,0.67401,0.563221,0.44102,1.62502,0.248069,0.81669,0.0402326,0.13793,0.503505,0.776656,1.61314,1.21607,0.741657,0.635967,0.480173,0.341918,0.192136,0.328551,1.45545,0.406714,0.147439,0.151399,0.0267963,0.563563,0.101804,0.229091,0.940968,0.799018,0.228998,0.368557,0.0993076,0.740521,0.547006,0.419845,0.331484,0.934619,0.241648,0.0333885,0.225998,0.109846
|tfbs_overrepresentation_jaspar=MA0003.1;0.000369852,MA0004.1;0.478761,MA0006.1;0.0694838,MA0007.1;0.146569,MA0009.1;0.526253,MA0014.1;0.00921962,MA0017.1;1.03696,MA0019.1;0.262545,MA0024.1;0.434294,MA0025.1;0.647545,MA0027.1;2.09389,MA0028.1;0.562332,MA0029.1;0.450974,MA0030.1;0.441064,MA0031.1;1.00334,MA0038.1;0.648449,MA0040.1;0.456051,MA0041.1;0.170492,MA0042.1;0.149889,MA0043.1;0.526535,MA0046.1;0.516541,MA0048.1;0.00505311,MA0050.1;0.150446,MA0051.1;0.22589,MA0052.1;0.459414,MA0055.1;0.00831201,MA0056.1;0,MA0057.1;0.0257204,MA0058.1;0.682118,MA0059.1;0.678862,MA0060.1;1.15812,MA0061.1;0.0847828,MA0063.1;0,MA0066.1;0.22927,MA0067.1;0.820123,MA0068.1;0.149869,MA0069.1;0.51311,MA0070.1;0.503171,MA0071.1;0.201311,MA0072.1;0.499187,MA0073.1;4.99807e-07,MA0074.1;0.639966,MA0076.1;0.356648,MA0077.1;0.49237,MA0078.1;0.30111,MA0081.1;0.331815,MA0083.1;0.532971,MA0084.1;0.999884,MA0087.1;0.497023,MA0088.1;0.42447,MA0089.1;0,MA0090.1;0.118716,MA0091.1;0.482932,MA0092.1;0.136418,MA0093.1;0.530993,MA0095.1;0,MA0098.1;0,MA0100.1;0.239133,MA0101.1;0.0724124,MA0103.1;0.232452,MA0105.1;0.274046,MA0106.1;0.719625,MA0107.1;0.041912,MA0108.2;0.997711,MA0109.1;0,MA0111.1;0.126618,MA0113.1;0.74833,MA0114.1;0.358913,MA0115.1;0.747865,MA0116.1;0.0431675,MA0117.1;0.560027,MA0119.1;0.308642,MA0122.1;0.583485,MA0124.1;0.70896,MA0125.1;0.631059,MA0130.1;0,MA0131.1;0.315517,MA0132.1;0,MA0133.1;0,MA0135.1;0.553498,MA0136.1;1.91093,MA0139.1;0.0745458,MA0140.1;0.199454,MA0141.1;0.329072,MA0142.1;0.359701,MA0143.1;0.74864,MA0144.1;1.34149,MA0145.1;0.315356,MA0146.1;0.00192039,MA0147.1;0.170045,MA0148.1;0.99741,MA0149.1;0.562525,MA0062.2;0.968423,MA0035.2;0.198962,MA0039.2;7.69028e-06,MA0138.2;0.816468,MA0002.2;0.459473,MA0137.2;1.45562,MA0104.2;0.264352,MA0047.2;0.698519,MA0112.2;0.891648,MA0065.2;0.0977819,MA0150.1;0.115337,MA0151.1;0,MA0152.1;2.47131,MA0153.1;0.615584,MA0154.1;0.0620528,MA0155.1;0.00116092,MA0156.1;0.58361,MA0157.1;0.89541,MA0158.1;0,MA0159.1;0.170777,MA0160.1;0.18494,MA0161.1;0,MA0162.1;0.000506716,MA0163.1;0.0941035,MA0164.1;0.28168,MA0080.2;1.88622,MA0018.2;0.260646,MA0099.2;0.204301,MA0079.2;3.10495e-09,MA0102.2;1.03595,MA0258.1;0.308654,MA0259.1;0.179817,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


Full id: C439_acute_CD14_Macrophage_biphenotypic_neuroblastoma_Monocytederived_myelodysplastic



Phase1 CAGE Peaks

Hg19::chr10:112206899..112206910,-p@chr10:112206899..112206910
-
Hg19::chr10:112206925..112206940,-p@chr10:112206925..112206940
-
Hg19::chr11:4475700..4475705,+p@chr11:4475700..4475705
+
Hg19::chr12:12869857..12869890,+p5@CDKN1B
Hg19::chr13:32388796..32388841,-p@chr13:32388796..32388841
-
Hg19::chr13:88463369..88463374,-p3@BC040238
Hg19::chr13:90031645..90031658,-p@chr13:90031645..90031658
-
Hg19::chr13:90031665..90031668,-p@chr13:90031665..90031668
-
Hg19::chr13:90436412..90436420,+p@chr13:90436412..90436420
+
Hg19::chr13:90436562..90436573,+p@chr13:90436562..90436573
+
Hg19::chr13:90494305..90494309,+p@chr13:90494305..90494309
+
Hg19::chr13:90526930..90526934,+p@chr13:90526930..90526934
+
Hg19::chr13:90531106..90531112,+p@chr13:90531106..90531112
+
Hg19::chr16:85935894..85935904,+p9@IRF8
Hg19::chr18:20407272..20407304,-p@chr18:20407272..20407304
-
Hg19::chr1:38969182..38969229,-p@chr1:38969182..38969229
-
Hg19::chr2:119710557..119710561,-p1@ENST00000556770
Hg19::chr2:60754889..60754902,-p2@uc002sag.2
Hg19::chr3:21584319..21584331,+p4@ZNF385D-AS1
Hg19::chr7:27205043..27205050,-p5@HOXA9
Hg19::chr7:27205066..27205067,-p7@HOXA9
Hg19::chr9:30349695..30349701,-p@chr9:30349695..30349701
-


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:0048102autophagic cell death0.0132419139814746
GO:0007275multicellular organismal development0.0132419139814746
GO:0031324negative regulation of cellular metabolic process0.0132419139814746
GO:0005072transforming growth factor beta receptor, cytoplasmic mediator activity0.0132419139814746
GO:0009892negative regulation of metabolic process0.0132419139814746
GO:0005071transmembrane receptor protein serine/threonine kinase signaling protein activity0.0132419139814746
GO:0031116positive regulation of microtubule polymerization0.0132419139814746
GO:0031112positive regulation of microtubule polymerization or depolymerization0.0132419139814746
GO:0031113regulation of microtubule polymerization0.0132419139814746
GO:0045736negative regulation of cyclin-dependent protein kinase activity0.0132419139814746
GO:0046785microtubule polymerization0.0132419139814746
GO:0032502developmental process0.0132419139814746
GO:0050680negative regulation of epithelial cell proliferation0.0132419139814746
GO:0042326negative regulation of phosphorylation0.0132419139814746
GO:0045936negative regulation of phosphate metabolic process0.0133886521848548
GO:0051130positive regulation of cellular component organization and biogenesis0.0135169912685775
GO:0004861cyclin-dependent protein kinase inhibitor activity0.013630178137687
GO:0032501multicellular organismal process0.0138347601184434
GO:0031323regulation of cellular metabolic process0.0142823592713417
GO:0019222regulation of metabolic process0.0159409183996984
GO:0051271negative regulation of cell motility0.0168473917503124
GO:0040013negative regulation of locomotion0.0168473917503124
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0181276571780347
GO:0031110regulation of microtubule polymerization or depolymerization0.0185223108448601
GO:0050678regulation of epithelial cell proliferation0.0185223108448601
GO:0031109microtubule polymerization or depolymerization0.0185223108448601
GO:0050673epithelial cell proliferation0.0185223108448601
GO:0000082G1/S transition of mitotic cell cycle0.0185223108448601
GO:0048523negative regulation of cellular process0.0185223108448601
GO:0048513organ development0.0185223108448601
GO:0048839inner ear development0.0185223108448601
GO:0004860protein kinase inhibitor activity0.0185223108448601
GO:0048519negative regulation of biological process0.0185223108448601
GO:0019210kinase inhibitor activity0.0185223108448601
GO:0043583ear development0.0185223108448601
GO:0000079regulation of cyclin-dependent protein kinase activity0.0210047719963499
GO:0030308negative regulation of cell growth0.0212837253173523
GO:0050794regulation of cellular process0.0212837253173523
GO:0045792negative regulation of cell size0.0212837253173523
GO:0006469negative regulation of protein kinase activity0.0212837253173523
GO:0033673negative regulation of kinase activity0.0212837253173523
GO:0051348negative regulation of transferase activity0.0212837253173523
GO:0045926negative regulation of growth0.0212837253173523
GO:0042325regulation of phosphorylation0.0212837253173523
GO:0003700transcription factor activity0.0212837253173523
GO:0005634nucleus0.0212837253173523
GO:0050789regulation of biological process0.0212837253173523
GO:0051174regulation of phosphorus metabolic process0.0212837253173523
GO:0019220regulation of phosphate metabolic process0.0212837253173523
GO:0051270regulation of cell motility0.0212837253173523
GO:0040012regulation of locomotion0.0214018511426233
GO:0040011locomotion0.0214018511426233
GO:0048731system development0.0214018511426233
GO:0030099myeloid cell differentiation0.0219868582700736
GO:0051329interphase of mitotic cell cycle0.0234601208300242
GO:0007423sensory organ development0.0234601208300242
GO:0043086negative regulation of catalytic activity0.0234601208300242
GO:0065007biological regulation0.0234601208300242
GO:0051325interphase0.0235120435595065
GO:0048869cellular developmental process0.0235519771064894
GO:0030154cell differentiation0.0235519771064894
GO:0051258protein polymerization0.024109619292839
GO:0051128regulation of cellular component organization and biogenesis0.0241787107162548
GO:0007050cell cycle arrest0.0241787107162548
GO:0000226microtubule cytoskeleton organization and biogenesis0.0241787107162548
GO:0019887protein kinase regulator activity0.0245105635014252
GO:0048856anatomical structure development0.0262090200083905
GO:0019207kinase regulator activity0.027627480156269
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0283387694782635
GO:0050954sensory perception of mechanical stimulus0.0286205475494717
GO:0007605sensory perception of sound0.0286205475494717
GO:0030097hemopoiesis0.0341326831092626
GO:0001558regulation of cell growth0.0341326831092626
GO:0048534hemopoietic or lymphoid organ development0.0359461017745621
GO:0005057receptor signaling protein activity0.0362825827367684
GO:0002520immune system development0.036811198128807
GO:0043231intracellular membrane-bound organelle0.0385003076234806
GO:0043227membrane-bound organelle0.0385003076234806
GO:0016049cell growth0.0385003076234806
GO:0040008regulation of growth0.0385003076234806
GO:0045892negative regulation of transcription, DNA-dependent0.0385003076234806
GO:0008361regulation of cell size0.0385894082372106
GO:0006917induction of apoptosis0.0389426403976106
GO:0012502induction of programmed cell death0.0389426403976106
GO:0045786negative regulation of progression through cell cycle0.0401657058010235
GO:0008285negative regulation of cell proliferation0.0401657058010235
GO:0008284positive regulation of cell proliferation0.0411060267430774
GO:0045859regulation of protein kinase activity0.0413316983284109
GO:0043549regulation of kinase activity0.041723320584043
GO:0051338regulation of transferase activity0.0421059891855547
GO:0006813potassium ion transport0.0425485939208282
GO:0043065positive regulation of apoptosis0.0425485939208282
GO:0043068positive regulation of programmed cell death0.0425485939208282
GO:0003702RNA polymerase II transcription factor activity0.0454941576303647
GO:0016481negative regulation of transcription0.0469347838142736
GO:0016563transcription activator activity0.0492155317148664
GO:0006355regulation of transcription, DNA-dependent0.0492155317148664
GO:0007017microtubule-based process0.0492155317148664
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0493123270482924
GO:0000278mitotic cell cycle0.0493123270482924
GO:0006351transcription, DNA-dependent0.0493123270482924
GO:0032774RNA biosynthetic process0.0493123270482924



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><br><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia7.41e-0831


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)
MA0003.10.000369852
MA0004.10.478761
MA0006.10.0694838
MA0007.10.146569
MA0009.10.526253
MA0014.10.00921962
MA0017.11.03696
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.562332
MA0029.10.450974
MA0030.10.441064
MA0031.11.00334
MA0038.10.648449
MA0040.10.456051
MA0041.10.170492
MA0042.10.149889
MA0043.10.526535
MA0046.10.516541
MA0048.10.00505311
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.00831201
MA0056.10
MA0057.10.0257204
MA0058.10.682118
MA0059.10.678862
MA0060.11.15812
MA0061.10.0847828
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.149869
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.14.99807e-07
MA0074.10.639966
MA0076.10.356648
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.42447
MA0089.10
MA0090.10.118716
MA0091.10.482932
MA0092.10.136418
MA0093.10.530993
MA0095.10
MA0098.10
MA0100.10.239133
MA0101.10.0724124
MA0103.10.232452
MA0105.10.274046
MA0106.10.719625
MA0107.10.041912
MA0108.20.997711
MA0109.10
MA0111.10.126618
MA0113.10.74833
MA0114.10.358913
MA0115.10.747865
MA0116.10.0431675
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.11.91093
MA0139.10.0745458
MA0140.10.199454
MA0141.10.329072
MA0142.10.359701
MA0143.10.74864
MA0144.11.34149
MA0145.10.315356
MA0146.10.00192039
MA0147.10.170045
MA0148.10.99741
MA0149.10.562525
MA0062.20.968423
MA0035.20.198962
MA0039.27.69028e-06
MA0138.20.816468
MA0002.20.459473
MA0137.21.45562
MA0104.20.264352
MA0047.20.698519
MA0112.20.891648
MA0065.20.0977819
MA0150.10.115337
MA0151.10
MA0152.12.47131
MA0153.10.615584
MA0154.10.0620528
MA0155.10.00116092
MA0156.10.58361
MA0157.10.89541
MA0158.10
MA0159.10.170777
MA0160.10.18494
MA0161.10
MA0162.10.000506716
MA0163.10.0941035
MA0164.10.28168
MA0080.21.88622
MA0018.20.260646
MA0099.20.204301
MA0079.23.10495e-09
MA0102.21.03595
MA0258.10.308654
MA0259.10.179817
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

No analysis results for this cluster

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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