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Coexpression cluster:C4586: Difference between revisions

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{{Coexpression_clusters
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(KEGG):04144!8.87028067484744e-05;0.00510444333379857;2;156;Phagosome (KEGG):04145!6.73840783266509e-05;0.00432850203411051;2;136;Cell adhesion molecules (CAMs) (KEGG):04514!2.20729154564608e-05;0.00174651943549246;2;78;Antigen processing and presentation (KEGG):04612!6.83807588327095e-05;0.00432850203411051;2;137;Natural killer cell mediated cytotoxicity (KEGG):04650!7.28240379719336e-06;0.00133235976771917;2;45;Type I diabetes mellitus (KEGG):04940!1.05241687813521e-05;0.00133235976771917;2;54;Autoimmune thyroid disease (KEGG):05320!5.45153351157612e-06;0.00133235976771917;2;39;Allograft rejection (KEGG):05330!6.64274556874299e-06;0.00133235976771917;2;43;Graft-versus-host disease (KEGG):05332!1.87899740683929e-05;0.00169915051218468;2;72;Viral myocarditis (KEGG):05416!1.48230348787841e-05;0.00156383017971173;2;64;Proteasome Degradation (Wikipathways):WP183!0.000948076017669582;0.046164009168065;2;511;Signaling in Immune system (Reactome):REACT_6900!9.37753775269525e-06;0.00133235976771917;2;51;{HLA-A,53} (Static 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1,0.04411,0.066952,0.089609,0.0367455,0.13497,0.204393,0.295769,0.286691,0.347036,0.141729,0.263159,0.255956,0.200105,0.227491,0.29837,0.253509,0.177664,0.28365,0.264413,0.131761,0.160658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,1.53533,0.743951,1.00973,0.409304,0.842925,0.645155,1.00813,0.795576,1.21459,1.3235,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,1.55608,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,1.23315,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,1.06461,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,1.50815,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.56135|tfbs_overrepresentation_jaspar=MA0003.1;0.401049,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,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;2.16573,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.67416,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;3.15662,MA0061.1;5.21573,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;0.211629,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;0.257905,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;3.21605,MA0106.1;0.986396,MA0107.1;4.63461,MA0108.2;1.15387,MA0109.1;0,MA0111.1;1.80901,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;0.752137,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;0.195278,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,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;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;1.29138,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4586_Eosinophils_CD14_myeloma_renal_CD4_smallcell_Neutrophils
|id=C4586
}}

Latest revision as of 14:15, 17 September 2013


Full id: C4586_Eosinophils_CD14_myeloma_renal_CD4_smallcell_Neutrophils



Phase1 CAGE Peaks

Hg19::chr6:29910301..29910324,+p1@HLA-A
Hg19::chr6:31324982..31324995,-p2@HLA-B
Hg19::chr6:31430954..31430968,+p1@HCP5


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
0.0001517463875231860.008004621941848052204Endocytosis (KEGG):04144
8.87028067484744e-050.005104443333798572156Phagosome (KEGG):04145
6.73840783266509e-050.004328502034110512136Cell adhesion molecules (CAMs) (KEGG):04514
2.20729154564608e-050.00174651943549246278Antigen processing and presentation (KEGG):04612
6.83807588327095e-050.004328502034110512137Natural killer cell mediated cytotoxicity (KEGG):04650
7.28240379719336e-060.00133235976771917245Type I diabetes mellitus (KEGG):04940
1.05241687813521e-050.00133235976771917254Autoimmune thyroid disease (KEGG):05320
5.45153351157612e-060.00133235976771917239Allograft rejection (KEGG):05330
6.64274556874299e-060.00133235976771917243Graft-versus-host disease (KEGG):05332
1.87899740683929e-050.00169915051218468272Viral myocarditis (KEGG):05416
1.48230348787841e-050.00156383017971173264Proteasome Degradation (Wikipathways):WP183
0.0009480760176695820.0461640091680652511Signaling in Immune system (Reactome):REACT_6900
9.37753775269525e-060.00133235976771917251{HLA-A,53} (Static Module):NA



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

No GOStat results

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
leukocyte1.05e-47136
nongranular leukocyte4.74e-41115
hematopoietic lineage restricted progenitor cell2.55e-38120
hematopoietic stem cell3.40e-30168
angioblastic mesenchymal cell3.40e-30168
hematopoietic cell2.77e-29177
hematopoietic oligopotent progenitor cell1.14e-28161
hematopoietic multipotent progenitor cell1.14e-28161
myeloid leukocyte1.38e-2672
defensive cell1.04e-2348
phagocyte1.04e-2348
macrophage dendritic cell progenitor5.66e-2361
granulocyte monocyte progenitor cell1.82e-2267
monopoietic cell1.83e-2259
monocyte1.83e-2259
monoblast1.83e-2259
promonocyte1.83e-2259
classical monocyte7.97e-2242
CD14-positive, CD16-negative classical monocyte7.97e-2242
myeloid lineage restricted progenitor cell1.75e-2066
lymphocyte7.37e-1753
common lymphoid progenitor7.37e-1753
lymphoid lineage restricted progenitor cell1.25e-1652
nucleate cell1.23e-1555
myeloid cell9.67e-13108
common myeloid progenitor9.67e-13108
mature alpha-beta T cell3.30e-1018
alpha-beta T cell3.30e-1018
immature T cell3.30e-1018
mature T cell3.30e-1018
immature alpha-beta T cell3.30e-1018
mesenchymal cell1.76e-09354
connective tissue cell1.91e-08361
T cell2.77e-0825
pro-T cell2.77e-0825
lymphocyte of B lineage3.94e-0824
pro-B cell3.94e-0824
stuff accumulating cell1.01e-0787
CD8-positive, alpha-beta T cell9.96e-0711
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.65e-29108
hematopoietic system3.21e-2998
blood island3.21e-2998
immune system1.22e-2293
bone marrow1.94e-2076
bone element9.95e-1982
skeletal element5.65e-1590
skeletal system2.97e-12100
lateral plate mesoderm5.78e-10203
connective tissue2.41e-08371
blood4.22e-0815
haemolymphatic fluid4.22e-0815
organism substance4.22e-0815


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)
MA0003.10.401049
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
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
MA0038.12.16573
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.67416
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.13.15662
MA0061.15.21573
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
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
MA0105.13.21605
MA0106.10.986396
MA0107.14.63461
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.11.29138
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
HNF4A#3172215.42152690863580.005444210486686610.0246900820278372
NFKB1#479035.488063424193840.006049381815655430.0270678800156479
NFYA#4800212.28372046655370.008516011403724430.0324955686881102
NFYB#4801211.17319550235760.01025467135054530.0381582506566287
POU2F2#545239.106124057742520.001324165192682130.00885368044548841
RFX5#5993312.04791082719510.0005717246050312580.00486438664153642
SP1#666735.69838137814090.005403962701712170.024770000465399
YY1#752834.911170749853860.008441455341808260.0331024351159506



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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