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Coexpression cluster:C1598: Difference between revisions

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{{Coexpression_clusters
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small ribosomal subunit (sensu Eukaryota)!0.0405039444248204!6189$GO:0005830!cytosolic ribosome (sensu Eukaryota)!0.0405039444248204!6189$GO:0006413!translational initiation!0.0405039444248204!6189$GO:0015935!small ribosomal subunit!0.0405039444248204!6189$GO:0022618!protein-RNA complex assembly!0.0405039444248204!6189$GO:0044445!cytosolic part!0.0405039444248204!6189$GO:0006917!induction of apoptosis!0.0405039444248204!6189$GO:0012502!induction of programmed cell death!0.0405039444248204!6189$GO:0033279!ribosomal subunit!0.0405039444248204!6189$GO:0022613!ribonucleoprotein complex biogenesis and assembly!0.0405039444248204!6189$GO:0043065!positive regulation of apoptosis!0.0405039444248204!6189$GO:0043068!positive regulation of programmed cell 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53,0.0972854,0.333309,0.249919,0.339517,0.303699,0.198326,0.394084,0.458518,0.282501,0.252005,0.390891,0.238377,0.334983,0.197875,0.287909,0.289389,0.117618,0.392533,0.396962,0.316002,0.330317,0.321404,0.225079,0.300542,0.379651,0.185715,0.345505,0.375521,0.271405,0.311201,0.221943,0.306427,0.367733,0.246925,0.208775,0.390438,0.343014,0.270094,0.276922,0.156279,0.313647,0.461742,0.422872,0.336468,0.13327,0.313545,0.17149,0.0877361,0.0880065,0.238969,0.126615,0.0669467,0.0879453,0.474066,0.396935,0.326779,0.292869,0.358198,0.29552,0.131776,0.158116,0.104606,0.194814,0.104167,0.168186,0.108081,0.123829,0.205215,0.175247,0.0724304,0.109077,0.144842,0.0604892,0.214671,0.316879,0.442567,0.430541,0.508546,0.224871,0.398887,0.389061,0.310732,0.349611,0.445995,0.385709,0.278202,0.426488,0.400591,0.209809,0.253154,0.319519,0.309489,0.430805,0.362154,0.480785,0.185476,0.336314,0.344469,0.184651,0.303359,0.297596,0.42392,0.425912,0.0840133,0.259046,0.345068,0.151046,0.483953,0.347171,0.321735,0.15463,0.13907,0.470121,0.269432,0.250466,0.409882,0.115686,0.408975,0.162633,0.342661,0.27567,0.248127,0.33299,0.384731,0.319112,0.526476|tfbs_overrepresentation_for_novel_motifs=0.508327,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.106358,1.50573,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,1.55551,0.44943,0.549618,0.802434,1.29435,0.642741,0.458349,0.233785,1.45697,1.00172,0.359091,0.27659,0.417272,0.0526856,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.218848,1.32072,0.734485,0.609718,0.785708,0.458489,0.817229,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,2.15436,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,1.58259,0.189341,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.796279,0.934302,0.755403,0.327263,1.18161,0.251545,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.084145,0.596731,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,1.44357,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,0.126633,1.15522,0.840171,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.233587|tfbs_overrepresentation_jaspar=MA0003.1;0.0497246,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.161847,MA0017.1;1.24112,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.0853006,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.412364,MA0089.1;0,MA0090.1;0.556637,MA0091.1;1.52322,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;1.77562,MA0101.1;1.16366,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;0.985964,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;0.504689,MA0122.1;1.17777,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;1.29278,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.143698,MA0146.1;0.333008,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;1.63245,MA0062.2;0.777733,MA0035.2;0.691506,MA0039.2;0.0575907,MA0138.2;0.837782,MA0002.2;2.29226,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.136971,MA0065.2;0.449243,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;0.130813,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;1.00463,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.000396307,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1598_CD34_CD133_CD4_CD8_Smooth_Cardiac_acute
|id=C1598
}}

Latest revision as of 11:48, 17 September 2013


Full id: C1598_CD34_CD133_CD4_CD8_Smooth_Cardiac_acute



Phase1 CAGE Peaks

Hg19::chr10:89705236..89705239,+p1@ENST00000395256
Hg19::chr17:37011443..37011449,+p1@ENST00000462007
Hg19::chr4:138369206..138369216,+p1@ENST00000463671
Hg19::chr4:152020736..152020788,+p1@RPS3A
Hg19::chr9:74204452..74204456,+p1@ENST00000437667


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:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0405039444248204
GO:0005830cytosolic ribosome (sensu Eukaryota)0.0405039444248204
GO:0006413translational initiation0.0405039444248204
GO:0015935small ribosomal subunit0.0405039444248204
GO:0022618protein-RNA complex assembly0.0405039444248204
GO:0044445cytosolic part0.0405039444248204
GO:0006917induction of apoptosis0.0405039444248204
GO:0012502induction of programmed cell death0.0405039444248204
GO:0033279ribosomal subunit0.0405039444248204
GO:0022613ribonucleoprotein complex biogenesis and assembly0.0405039444248204
GO:0043065positive regulation of apoptosis0.0405039444248204
GO:0043068positive regulation of programmed cell death0.0405039444248204



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
hematopoietic lineage restricted progenitor cell9.47e-24120
hematopoietic stem cell1.47e-21168
angioblastic mesenchymal cell1.47e-21168
leukocyte1.68e-21136
nongranular leukocyte4.48e-21115
hematopoietic oligopotent progenitor cell6.64e-21161
hematopoietic multipotent progenitor cell6.64e-21161
hematopoietic cell5.89e-19177
classical monocyte5.35e-1842
CD14-positive, CD16-negative classical monocyte5.35e-1842
defensive cell6.45e-1648
phagocyte6.45e-1648
myeloid lineage restricted progenitor cell8.62e-1466
macrophage dendritic cell progenitor4.51e-1361
granulocyte monocyte progenitor cell8.63e-1367
monopoietic cell3.15e-1259
monocyte3.15e-1259
monoblast3.15e-1259
promonocyte3.15e-1259
myeloid cell1.43e-11108
common myeloid progenitor1.43e-11108
stuff accumulating cell1.73e-1187
nucleate cell1.48e-1055
myeloid leukocyte2.08e-1072
stem cell3.80e-10441
native cell5.28e-10722
lymphocyte1.30e-0953
common lymphoid progenitor1.30e-0953
lymphoid lineage restricted progenitor cell2.01e-0952
multi fate stem cell3.23e-09427
somatic stem cell3.56e-09433
mesenchymal cell3.59e-09354
connective tissue cell6.75e-09361
animal cell2.52e-08679
eukaryotic cell2.52e-08679
motile cell3.19e-08386
Uber Anatomy
Ontology termp-valuen
skeletal element4.55e-1290
bone marrow7.03e-1276
bone element1.26e-1182
skeletal system1.60e-10100
immune system2.22e-0993
connective tissue1.38e-08371
hematopoietic system6.17e-0898
blood island6.17e-0898
musculoskeletal system1.30e-07167
hemolymphoid system9.69e-07108


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)
MA0003.10.0497246
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.0853006
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.11.52322
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.11.16366
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.985964
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.11.29278
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.333008
MA0147.10.386018
MA0148.10.653474
MA0149.11.63245
MA0062.20.777733
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.22.29226
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.449243
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.11.00463
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.000396307
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
KAT2A#26481123.2180.008089481544540810.0319912667283993



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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