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Coexpression cluster:C3568: Difference between revisions

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{{Coexpression_clusters
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4162e-05,0.00170684,0.17639,0.0779009,0.276869,0.205298,0.0337138,0.0192444,0.258854,0.188263,0.0719199,0.264884,0.162568,0.19104,3.62915e-05,0.219428,0.0233135,0.0900729,0.0953646,0.166124,0.252184,0.378361,0.255516,0.20753,0.447185,0.0171537,0.193601,0.0264253,0.222977,0.0664606,0.310674,0.21801,0.0211771,0.0186488,0.123324,0.199468,0.0325925,0.0933115,0.12405,0.179889,0.226869,0.00455899,0.0855609,0.131118,0.20837,0.247588,0.222339,0.0673329,0.20847,0.266544,0.113092,0.145701,0.229428,0.162145,0.228955,0.000916623,0.0384949,0.0660995,0.0521984,0.0455518,0.268741,0.201602,0.350452,0.154941,0.120196,0.0986735,0.108462,0.0595618,0.21593,0.158479,0.220319,0.195218,0.124213,0.0370716,0.30793,0.180606,0.159884,0.257294,0.150733,0.217112,0.123917,0.184317,0.185335,0.0723291,0.258496,0.261744,0.203781,0.21382,0.207559,0.141867,0.193031,0.0339803,0.115972,0.224568,0.246105,0.0159159,0.200432,0.139785,0.197112,0.240478,0.156465,0.13108,0.256963,0.222798,0.172134,0.176789,0.0969345,0.202137,0.310405,0.0437875,0.218161,0.0822373,0.202065,0.106739,0.0536053,0.0537737,0.15113,0.078016,0.0407233,0.0537355,0.319922,0.0377035,0.211332,0.187731,0.0297055,0.00132285,0.0812887,0.0981146,0.064145,0.121913,0.0638699,0.104603,0.0663259,0.0762523,0.128736,0.109171,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.0488311,0.286691,0.347036,0.141729,0.263159,0.0359756,0.200105,0.227491,0.0497481,0.0352561,0.177664,0.28365,0.264413,0.00908908,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.0203812,0.190993,0.0440463,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,1.18324,0.598234,0.777097,0.718382,0.63803,0.461452,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,1.5923,1.45054,1.10051,1.87308,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,2.95969,3.14048,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,1.63757,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,1.54007,1.29196,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,1.42224|tfbs_overrepresentation_jaspar=MA0003.1;2.61626,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;1.62115,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;2.37507,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;1.23283,MA0061.1;2.01615,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;3.33427,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;1.55947,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;1.36919,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;1.51687,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;1.38935,MA0160.1;0.871361,MA0161.1;0,MA0162.1;2.05956,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;4.10519,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C3568_Mast_Eosinophils_CD4_immature_CD8_Neutrophils_Natural
|gostat_on_coexpression_clusters=GO:0007049!cell cycle!0.0463706779592514!8556;1540$GO:0016788!hydrolase activity, acting on ester bonds!0.0463706779592514!8556;1540$GO:0005856!cytoskeleton!0.0469426303635197!8556;1540$GO:0008138!protein tyrosine/serine/threonine phosphatase activity!0.049963050018113!8556$GO:0043687!post-translational protein modification!0.049963050018113!8556;1540$GO:0006464!protein modification process!0.049963050018113!8556;1540$GO:0043412!biopolymer modification!0.049963050018113!8556;1540$GO:0043232!intracellular non-membrane-bound organelle!0.049963050018113!8556;1540$GO:0043228!non-membrane-bound organelle!0.049963050018113!8556;1540$GO:0005813!centrosome!0.049963050018113!8556$GO:0004221!ubiquitin thiolesterase activity!0.049963050018113!1540$GO:0004843!ubiquitin-specific protease activity!0.049963050018113!1540$GO:0019783!small conjugating protein-specific protease activity!0.049963050018113!1540$GO:0005815!microtubule organizing center!0.049963050018113!8556
|id=C3568
}}

Latest revision as of 12:28, 17 September 2013


Full id: C3568_Mast_Eosinophils_CD4_immature_CD8_Neutrophils_Natural



Phase1 CAGE Peaks

Hg19::chr16:50776050..50776074,+p3@CYLD
Hg19::chr1:100818080..100818094,+p2@CDC14A
Hg19::chr9:2017714..2017737,+p@chr9:2017714..2017737
+


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:0007049cell cycle0.0463706779592514
GO:0016788hydrolase activity, acting on ester bonds0.0463706779592514
GO:0005856cytoskeleton0.0469426303635197
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.049963050018113
GO:0043687post-translational protein modification0.049963050018113
GO:0006464protein modification process0.049963050018113
GO:0043412biopolymer modification0.049963050018113
GO:0043232intracellular non-membrane-bound organelle0.049963050018113
GO:0043228non-membrane-bound organelle0.049963050018113
GO:0005813centrosome0.049963050018113
GO:0004221ubiquitin thiolesterase activity0.049963050018113
GO:0004843ubiquitin-specific protease activity0.049963050018113
GO:0019783small conjugating protein-specific protease activity0.049963050018113
GO:0005815microtubule organizing center0.049963050018113



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
leukocyte6.91e-31136
hematopoietic stem cell1.03e-28168
angioblastic mesenchymal cell1.03e-28168
hematopoietic cell3.46e-27177
hematopoietic oligopotent progenitor cell4.36e-26161
hematopoietic multipotent progenitor cell4.36e-26161
hematopoietic lineage restricted progenitor cell3.08e-23120
nongranular leukocyte5.74e-22115
myeloid leukocyte6.22e-1672
myeloid cell1.32e-14108
common myeloid progenitor1.32e-14108
granulocyte monocyte progenitor cell2.98e-1367
mature alpha-beta T cell1.22e-1218
alpha-beta T cell1.22e-1218
immature T cell1.22e-1218
mature T cell1.22e-1218
immature alpha-beta T cell1.22e-1218
myeloid lineage restricted progenitor cell1.77e-1166
lymphocyte2.54e-1153
common lymphoid progenitor2.54e-1153
lymphoid lineage restricted progenitor cell2.93e-1152
nucleate cell1.11e-1055
macrophage dendritic cell progenitor1.58e-1061
classical monocyte2.44e-1042
CD14-positive, CD16-negative classical monocyte2.44e-1042
monopoietic cell9.75e-1059
monocyte9.75e-1059
monoblast9.75e-1059
promonocyte9.75e-1059
T cell8.24e-0925
pro-T cell8.24e-0925
defensive cell2.29e-0848
phagocyte2.29e-0848
CD8-positive, alpha-beta T cell2.37e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.11e-1998
blood island1.11e-1998
hemolymphoid system1.19e-19108
adult organism8.02e-17114
immune system1.37e-1393
bone marrow4.98e-1176
bone element8.14e-1182
skeletal element1.00e-0890
blood2.41e-0815
haemolymphatic fluid2.41e-0815
organism substance2.41e-0815
skeletal system2.65e-07100
lateral plate mesoderm8.19e-07203


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)
MA0003.12.61626
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.12.37507
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.11.23283
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.13.33427
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.11.36919
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
ELF1#199734.258097958807540.01295179875054610.0461426883748348
SIN3A#2594235.408884726815140.006318961977991520.027619740102932
YY1#752834.911170749853860.008441455341808260.0328802131221092



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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