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Coexpression cluster:C916: Difference between revisions

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{{Coexpression_clusters
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regulation of progression through cell cycle!0.00278412055790254!8522;864$GO:0000074!regulation of progression through cell cycle!0.00278412055790254!8522;864$GO:0051726!regulation of cell cycle!0.00278412055790254!8522;864$GO:0022402!cell cycle process!0.00633631022849388!8522;864$GO:0007049!cell cycle!0.00882937210526807!8522;864$GO:0050680!negative regulation of epithelial cell proliferation!0.00882937210526807!864$GO:0048523!negative regulation of cellular process!0.0113398994525439!8522;864$GO:0048519!negative regulation of biological process!0.0113398994525439!8522;864$GO:0050678!regulation of epithelial cell proliferation!0.0132663844202363!864$GO:0050673!epithelial cell proliferation!0.0132663844202363!864$GO:0003700!transcription factor activity!0.0132663844202363!8522;864$GO:0048869!cellular developmental process!0.0163683765033966!8522;864$GO:0030154!cell differentiation!0.0163683765033966!8522;864$GO:0007050!cell cycle arrest!0.0318070797147764!8522$GO:0032502!developmental process!0.0485201580171879!8522;864$GO:0003677!DNA 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85334,0.0251732,0.326222,0.144568,0.0946253,0.254626,0.327893,0.448409,0.537875,0.000535795,0.235347,0.344033,0.000790426,0.574041,0.174916,0.188703,0.504091,0.0149909,0.302353,0.37651,0.184705,0.411826,0.184047,0.425621,0.111096,0.18548,0.0116267,0.00891526,0.608967,0.49107,0.725948,0.396522,0.318983,0.267772,0.291371,0.168254,0.51798,0.40407,0.172158,0.478764,0.00781401,0.594172,0.302509,0.449854,0.40705,0.590314,0.387463,0.520157,0.327588,0.457295,0.459324,0.201671,0.226502,0.0645793,0.495225,0.51408,0.502377,0.368078,0.136392,0.576606,0.00640381,0.533737,0.208377,0.112108,0.488829,0.363467,0.482434,0.561852,0.399782,0.343945,0.224236,0.530537,0.432612,0.44213,0.263525,0.148007,0.0268601,0.0035006,0.522084,0.226979,0.147915,0.287253,0.152349,0.152802,0.38832,0.216263,0.117262,0.152699,0.03013,0.064566,0.160066,0.46408,0.00139799,0.132054,0.22458,0.00393544,0.180355,0.322962,0.179632,0.282128,0.186072,0.211757,0.338622,0.29306,0.126579,0.187708,0.245457,0.106235,0.352719,0.150936,0.0045199,0.269216,0.721601,0.367773,0.599943,0.588096,0.488202,0.0438035,0.654598,0.00209963,0.443905,0.0804409,0.601983,0.0680632,0.408688,0.0332857,0.486539,0.0829613,0.554869,0.0320422,0.0535082,0.0389145,0.176963,0.307503,0.138853,0.13384,0.629431,0.0801082,0.578048,0.41706,0.533176,0.255282,0.696023,0.53587,0.00571922,0.0374633,0.236266,0.6812,0.110542,0.015865,0.613018,0.198522,0.244611,0.273479,0.0411991,0.44039,0.401506,0.165914,0.21811,0.499348,0.389242|tfbs_overrepresentation_for_novel_motifs=0.312007,0.0494815,0.823567,0.440628,1.35412,0.439064,0.511871,0.492582,0.487494,0.0287394,0.410439,0.553754,0.40163,0.500805,1.34958,0.782718,0.728104,0.624077,0.426514,0.216842,0.305279,0.141777,1.10261,1.33716,0.347482,0.575764,0.729404,0.429643,0.270022,0.676,0.389837,0.764231,0.557092,0.129565,0.23642,0.452714,0.233607,0.440165,1.14973,0.14756,0.235191,0.374544,0.0412835,0.264644,0.0550925,0.333541,0.51292,0.4002,0.615516,0.743836,0.589559,1.30117,0.546719,0.839846,0.99088,0.503626,0.752594,1.18995,1.12004,0.47124,0.804523,0.5152,0.946802,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.504216,0.0724994,0.988898,0.124338,0.367887,0.69735,0.684401,0.750836,0.905375,0.436045,0.699894,0.532172,0.498312,0.937974,0.0150019,4.95999,1.61674,0.614883,1.54397,1.17124,0.911274,0.78075,0.196636,0.267904,0.598862,0.837326,0.82268,0.619373,0.0858425,0.214313,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,0.49749,0.347247,0.252953,0.315525,0.814459,0.812156,0.41935,1.12352,0.656078,0.0867932,0.388709,0.664981,1.09481,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,1.26174,0.785662,1.02292,1.13275,2.10644,1.01734,1.03718,1.33422,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,1.07409,0.50389,0.0382049,0.912334,0.471444,0.514733,1.31376,0.599133,2.01925,0.347536,0.320853,1.10357,2.06978,0.750062,0.323817,0.673453,0.531409,0.540317,0.510589,0.00185481|tfbs_overrepresentation_jaspar=MA0003.1;0.0913842,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.00594475,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;2.29414,MA0027.1;2.48103,MA0028.1;0.280275,MA0029.1;0.785955,MA0030.1;0.774581,MA0031.1;0.710608,MA0038.1;0.514558,MA0040.1;0.791764,MA0041.1;0.433167,MA0042.1;0.402577,MA0043.1;0.871285,MA0046.1;0.860127,MA0048.1;0.264106,MA0050.1;0.403421,MA0051.1;0.510444,MA0052.1;0.795605,MA0055.1;0.42489,MA0056.1;0,MA0057.1;0.539841,MA0058.1;0.86817,MA0059.1;0.865474,MA0060.1;0.162248,MA0061.1;0.139804,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.354973,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;4.2395,MA0074.1;1.27017,MA0076.1;0.339975,MA0077.1;0.832987,MA0078.1;0.607575,MA0081.1;0.324031,MA0083.1;0.878452,MA0084.1;1.37471,MA0087.1;0.838229,MA0088.1;1.4402,MA0089.1;0,MA0090.1;0.353576,MA0091.1;0.417885,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;0.271368,MA0103.1;0.714036,MA0105.1;1.29177,MA0106.1;0.554855,MA0107.1;0.205358,MA0108.2;0.707575,MA0109.1;0,MA0111.1;0.366362,MA0113.1;0.57094,MA0114.1;0.200901,MA0115.1;1.11137,MA0116.1;0.599942,MA0117.1;0.908433,MA0119.1;0.308914,MA0122.1;0.934245,MA0124.1;1.06995,MA0125.1;0.986127,MA0130.1;0,MA0131.1;0.625452,MA0132.1;0,MA0133.1;0,MA0135.1;0.90122,MA0136.1;0.521435,MA0139.1;0.129876,MA0140.1;0.474342,MA0141.1;0.861836,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.046841,MA0146.1;0.0045741,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;5.27504,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;1.17223,MA0138.2;0.608783,MA0002.2;1.45266,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.378721,MA0065.2;0.0483532,MA0150.1;0.34802,MA0151.1;0,MA0152.1;0.480711,MA0153.1;0.969315,MA0154.1;2.33732,MA0155.1;0.156896,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.60858,MA0160.1;0.453945,MA0161.1;0,MA0162.1;0.0107891,MA0163.1;0.604232,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.104637,MA0102.2;1.41188,MA0258.1;1.01999,MA0259.1;0.624802,MA0442.1;0}}
|full_id=C916_Natural_CD8_CD14_Basophils_Whole_Peripheral_CD4
|id=C916
}}

Latest revision as of 11:33, 17 September 2013


Full id: C916_Natural_CD8_CD14_Basophils_Whole_Peripheral_CD4



Phase1 CAGE Peaks

Hg19::chr17:10017864..10017880,-p16@GAS7
Hg19::chr17:10017891..10017924,-p9@GAS7
Hg19::chr17:10018796..10018825,+p@chr17:10018796..10018825
+
Hg19::chr1:25228796..25228804,-p@chr1:25228796..25228804
-
Hg19::chr1:25245820..25245840,-p@chr1:25245820..25245840
-
Hg19::chr1:25248726..25248732,-p@chr1:25248726..25248732
-
Hg19::chr1:25249270..25249275,-p@chr1:25249270..25249275
-
Hg19::chr1:25254150..25254174,-p2@EF491807
Hg19::chr1:25254177..25254220,-p1@EF491807


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:0045786negative regulation of progression through cell cycle0.00278412055790254
GO:0000074regulation of progression through cell cycle0.00278412055790254
GO:0051726regulation of cell cycle0.00278412055790254
GO:0022402cell cycle process0.00633631022849388
GO:0007049cell cycle0.00882937210526807
GO:0050680negative regulation of epithelial cell proliferation0.00882937210526807
GO:0048523negative regulation of cellular process0.0113398994525439
GO:0048519negative regulation of biological process0.0113398994525439
GO:0050678regulation of epithelial cell proliferation0.0132663844202363
GO:0050673epithelial cell proliferation0.0132663844202363
GO:0003700transcription factor activity0.0132663844202363
GO:0048869cellular developmental process0.0163683765033966
GO:0030154cell differentiation0.0163683765033966
GO:0007050cell cycle arrest0.0318070797147764
GO:0032502developmental process0.0485201580171879
GO:0003677DNA binding0.0499127809821499



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
leukocyte5.43e-76136
hematopoietic stem cell3.98e-68168
angioblastic mesenchymal cell3.98e-68168
nongranular leukocyte8.87e-68115
hematopoietic lineage restricted progenitor cell1.10e-66120
hematopoietic oligopotent progenitor cell2.98e-65161
hematopoietic multipotent progenitor cell2.98e-65161
hematopoietic cell3.07e-64177
classical monocyte3.52e-5242
CD14-positive, CD16-negative classical monocyte3.52e-5242
defensive cell1.33e-4348
phagocyte1.33e-4348
myeloid leukocyte4.31e-3672
granulocyte monocyte progenitor cell9.77e-3667
macrophage dendritic cell progenitor2.73e-3561
myeloid cell5.04e-34108
common myeloid progenitor5.04e-34108
monopoietic cell1.93e-3359
monocyte1.93e-3359
monoblast1.93e-3359
promonocyte1.93e-3359
myeloid lineage restricted progenitor cell3.80e-3366
lymphoid lineage restricted progenitor cell3.70e-2952
lymphocyte2.39e-2853
common lymphoid progenitor2.39e-2853
nucleate cell8.10e-2755
T cell2.80e-2025
pro-T cell2.80e-2025
stuff accumulating cell4.63e-1987
mature alpha-beta T cell1.01e-1818
alpha-beta T cell1.01e-1818
immature T cell1.01e-1818
mature T cell1.01e-1818
immature alpha-beta T cell1.01e-1818
mesenchymal cell2.31e-17354
connective tissue cell1.99e-16361
motile cell1.34e-14386
CD8-positive, alpha-beta T cell8.12e-1411
intermediate monocyte3.55e-119
CD14-positive, CD16-positive monocyte3.55e-119
multi fate stem cell2.23e-09427
somatic stem cell7.15e-09433
stem cell1.12e-08441
lymphocyte of B lineage7.76e-0824
pro-B cell7.76e-0824
Uber Anatomy
Ontology termp-valuen
hematopoietic system3.44e-4698
blood island3.44e-4698
hemolymphoid system3.97e-41108
immune system2.43e-3193
bone marrow7.57e-3176
bone element1.61e-2882
skeletal element1.73e-2490
skeletal system2.13e-20100
connective tissue3.68e-15371
lateral plate mesoderm1.42e-12203
blood7.22e-1115
haemolymphatic fluid7.22e-1115
organism substance7.22e-1115
musculoskeletal system6.09e-07167


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)
MA0003.10.0913842
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.00594475
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.12.29414
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.264106
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.42489
MA0056.10
MA0057.10.539841
MA0058.10.86817
MA0059.10.865474
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.354973
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.14.2395
MA0074.11.27017
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.11.4402
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.714036
MA0105.11.29177
MA0106.10.554855
MA0107.10.205358
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.10.211483
MA0148.10.439278
MA0149.15.27504
MA0062.20.135498
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.21.45266
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.378721
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.12.33732
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.0107891
MA0163.10.604232
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.104637
MA0102.21.41188
MA0258.11.01999
MA0259.10.624802
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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