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Coexpression cluster:C4155: Difference between revisions

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{{Coexpression_clusters
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,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.63186,1.91835,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,2.00385,0.305559,0.69094,0.680949,0.845342,0.635379,0.743951,1.00973,0.409304,0.842925,0.645155,0.388328,0.795576,1.21459,1.3235,0.439574,0.599922,1.36391,1.45286,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,3.41193,1.0078,0.891404,1.25741,2.16722,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,2.41357,1.45054,1.92922,0.414196,0.396746,1.12884,1.20029,0.73687,1.16162,1.14559,0.960908,1.24629,1.39759,2.95969,0.82001,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,1.90788,1.16312,0.921547,0.743661,3.73269,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,1.66424,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,1.73097,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,2.3415,2.79286,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,3.62109,0.524529,0.936473,5.4618|tfbs_overrepresentation_jaspar=MA0003.1;1.0927,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.758317,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;1.58389,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;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.190716,MA0056.1;0,MA0057.1;0.886807,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,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;0.0185922,MA0074.1;0.935474,MA0076.1;1.74184,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;2.84236,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;2.19699,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,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;1.12079,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;1.16674,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;2.07067,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.256269,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.8915,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.09178,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4155_granulocyte_CD14_CD14CD16_acute_CD4_Preadipocyte_CD133
|id=C4155
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4155_granulocyte_CD14_CD14CD16_acute_CD4_Preadipocyte_CD133



Phase1 CAGE Peaks

Hg19::chr2:182322231..182322262,+p2@ITGA4
Hg19::chr2:182322274..182322290,+p8@ITGA4
Hg19::chr2:182322344..182322359,+p6@ITGA4


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

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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell2.79e-55168
angioblastic mesenchymal cell2.79e-55168
hematopoietic cell3.39e-52177
hematopoietic oligopotent progenitor cell2.45e-51161
hematopoietic multipotent progenitor cell2.45e-51161
leukocyte1.46e-45136
multi fate stem cell1.93e-42427
stem cell2.19e-41441
connective tissue cell3.05e-41361
mesenchymal cell4.90e-41354
somatic stem cell1.72e-40433
nongranular leukocyte8.45e-39115
hematopoietic lineage restricted progenitor cell3.01e-37120
myeloid cell2.07e-36108
common myeloid progenitor2.07e-36108
motile cell2.78e-35386
myeloid leukocyte2.40e-2972
granulocyte monocyte progenitor cell1.81e-2567
myeloid lineage restricted progenitor cell1.31e-2466
defensive cell3.25e-2448
phagocyte3.25e-2448
monopoietic cell4.04e-2459
monocyte4.04e-2459
monoblast4.04e-2459
promonocyte4.04e-2459
classical monocyte4.78e-2442
CD14-positive, CD16-negative classical monocyte4.78e-2442
macrophage dendritic cell progenitor1.51e-2361
somatic cell4.91e-15588
stuff accumulating cell1.19e-1387
lymphocyte5.45e-1353
common lymphoid progenitor5.45e-1353
lymphoid lineage restricted progenitor cell6.77e-1352
nucleate cell1.48e-1255
native cell1.55e-07722
intermediate monocyte1.88e-079
CD14-positive, CD16-positive monocyte1.88e-079
mature alpha-beta T cell9.63e-0718
alpha-beta T cell9.63e-0718
immature T cell9.63e-0718
mature T cell9.63e-0718
immature alpha-beta T cell9.63e-0718
Uber Anatomy
Ontology termp-valuen
connective tissue1.58e-40371
hematopoietic system7.10e-3498
blood island7.10e-3498
hemolymphoid system1.84e-32108
immune system1.15e-2593
bone marrow1.10e-2476
bone element1.34e-2482
skeletal element5.28e-2290
skeletal system4.18e-18100
musculoskeletal system6.24e-17167
lateral plate mesoderm3.81e-13203
mesoderm1.57e-08315
mesoderm-derived structure1.57e-08315
presumptive mesoderm1.57e-08315
blood9.20e-0815
haemolymphatic fluid9.20e-0815
organism substance9.20e-0815
Disease
Ontology termp-valuen
hematologic cancer4.39e-0951
immune system cancer4.39e-0951
myeloid leukemia6.67e-0931
leukemia9.71e-0939


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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.10.886807
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.11.74184
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.12.84236
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.12.19699
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.752137
MA0146.11.16674
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
MA0112.22.07067
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.09178
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
BCLAF1#9774321.65264761012189.8473954032885e-050.0013937554255645
CTCF#1066435.360256373075030.0064925092527670.0280125247397229
EGR1#195834.988179094810140.008056488137383440.0321308880200172
ELF1#199734.258097958807540.01295179875054610.0463402846765428
GABPB1#255337.067683836182170.002832212825417420.0154437150980927
GATA1#2623313.56030814380040.0004009615963782630.00388496411208363
MEF2A#4205318.74323090964410.0001518243905622470.00195155538780683
MYC#460935.22228187160940.007020843755740150.0295129764944957
NANOG#79923329.24477848101273.99627955670032e-050.000738572713895284
NFKB1#479035.488063424193840.006049381815655430.0270100204114932
PAX5#507936.669565531177830.003370290999677260.0173240388677672
POU2F2#545239.106124057742520.001324165192682130.00883445052756669
RAD21#5885310.35503389545630.0009004912073565420.00665579626363127
SMC3#9126315.04493284493280.0002935825420371870.00309711788967896
SRF#6722313.79717826216780.0003806615025800190.00375658193971035
SUZ12#23512350.11578091106297.93834897779404e-060.000223109049755606
YY1#752834.911170749853860.008441455341808260.0330082427063204
ZEB1#6935316.88843201754390.0002075486917327580.00243142768546018
ZNF143#7702313.50087655222790.0004062804962997170.00389744913686471



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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