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Coexpression cluster:C4097: Difference between revisions

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{{Coexpression_clusters
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954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,1.40091,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,2.13378,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.680949,0.845342,1.53533,0.743951,1.00973,1.85641,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,1.95911,0.599922,0.427404,0.596053,0.855276,0.567465,1.18324,0.598234,0.777097,0.259059,0.63803,3.55152,0.726632,0.939121,0.808003,0.69206,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,0.396746,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,0.498519,1.39759,0.507157,0.303648,0.993996,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,1.44883,0.188952,0.794219,2.50498,0.547323,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,1.87432,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,1.51317,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,2.24188,0.936473,1.96295|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;0.377374,MA0017.1;1.64148,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;2.45333,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;1.06172,MA0056.1;0,MA0057.1;0.333427,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;1.04561,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;4.61448,MA0092.1;3.07926,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,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;3.4624,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;0.348055,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;3.37171,MA0138.2;2.38017,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.83144,MA0156.1;1.60572,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;5.63764,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.69213,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}}
|full_id=C4097_Neutrophils_Mast_Eosinophils_Macrophage_CD4_acute_Whole
|id=C4097
}}

Latest revision as of 12:39, 17 September 2013


Full id: C4097_Neutrophils_Mast_Eosinophils_Macrophage_CD4_acute_Whole



Phase1 CAGE Peaks

Hg19::chr22:37640236..37640252,-p2@RAC2
Hg19::chr22:37640254..37640276,-p3@RAC2
Hg19::chr22:37640277..37640327,-p1@RAC2


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 cell9.53e-62168
angioblastic mesenchymal cell9.53e-62168
hematopoietic cell7.80e-59177
hematopoietic oligopotent progenitor cell3.17e-58161
hematopoietic multipotent progenitor cell3.17e-58161
leukocyte2.75e-50136
hematopoietic lineage restricted progenitor cell3.50e-44120
nongranular leukocyte1.22e-43115
myeloid cell1.46e-34108
common myeloid progenitor1.46e-34108
myeloid leukocyte1.96e-2872
myeloid lineage restricted progenitor cell1.67e-2366
granulocyte monocyte progenitor cell3.69e-2367
monopoietic cell9.70e-2159
monocyte9.70e-2159
monoblast9.70e-2159
promonocyte9.70e-2159
lymphocyte1.13e-2053
common lymphoid progenitor1.13e-2053
lymphoid lineage restricted progenitor cell1.86e-2052
nucleate cell3.09e-2055
macrophage dendritic cell progenitor5.79e-2061
defensive cell1.33e-1948
phagocyte1.33e-1948
multi fate stem cell3.92e-17427
classical monocyte5.88e-1742
CD14-positive, CD16-negative classical monocyte5.88e-1742
somatic stem cell9.19e-17433
mesenchymal cell1.67e-16354
stem cell7.34e-16441
connective tissue cell1.20e-15361
somatic cell8.35e-13588
T cell3.48e-1125
pro-T cell3.48e-1125
lymphocyte of B lineage1.10e-0924
pro-B cell1.10e-0924
mature alpha-beta T cell3.81e-0918
alpha-beta T cell3.81e-0918
immature T cell3.81e-0918
mature T cell3.81e-0918
immature alpha-beta T cell3.81e-0918
motile cell6.18e-09386
endothelial cell9.18e-0936
endothelial cell of vascular tree1.46e-0824
native cell1.98e-07722
B cell3.11e-0714
blood vessel endothelial cell9.02e-0718
embryonic blood vessel endothelial progenitor cell9.02e-0718
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.89e-35108
lateral plate mesoderm4.30e-32203
hematopoietic system8.34e-3298
blood island8.34e-3298
immune system3.74e-2893
bone marrow7.89e-2276
bone element2.46e-1782
skeletal element1.00e-1590
connective tissue1.65e-14371
mesoderm8.46e-13315
mesoderm-derived structure8.46e-13315
presumptive mesoderm8.46e-13315
cardiovascular system1.65e-12109
circulatory system5.11e-12112
skeletal system9.40e-12100
vessel1.33e-1068
musculoskeletal system5.19e-10167
epithelial tube open at both ends3.31e-0859
blood vessel3.31e-0859
blood vasculature3.31e-0859
vascular cord3.31e-0859
blood3.64e-0815
haemolymphatic fluid3.64e-0815
organism substance3.64e-0815
splanchnic layer of lateral plate mesoderm5.73e-0883
vasculature1.67e-0778
vascular system1.67e-0778
artery5.10e-0742
arterial blood vessel5.10e-0742
arterial system5.10e-0742
blood vessel endothelium9.02e-0718
endothelium9.02e-0718
cardiovascular system endothelium9.02e-0718
Disease
Ontology termp-valuen
hematologic cancer2.59e-1451
immune system cancer2.59e-1451
leukemia2.00e-1239
myeloid leukemia2.83e-1031


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
MA0014.10.377374
MA0017.11.64148
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
MA0048.12.45333
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.11.06172
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
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
MA0091.14.61448
MA0092.13.07926
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
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
MA0116.13.4624
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
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.23.37171
MA0138.22.38017
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.83144
MA0156.11.60572
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.15.63764
MA0164.11.01792
MA0080.21.55139
MA0018.20.987913
MA0099.20.902716
MA0079.20.69213
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
E2F6#187635.017155731697390.00791769806886330.0322976396755854
EBF1#187938.9064668465690.00141523283560980.00916566427621557
EGR1#195834.988179094810140.008056488137383440.0321223014652283
ELF1#199734.258097958807540.01295179875054610.0463260012229283
ETS1#211339.728760922202340.001085840092584840.00763560822983219
FOS#235338.99795530889440.001372499272417130.00898867821608908
GABPB1#255337.067683836182170.002832212825417420.0154388786092056
IRF1#365937.63716375356390.002244692747297240.0128330121433642
MAX#414936.452555509007120.003721913834265510.0186899201335155
MYC#460935.22228187160940.007020843755740150.0295058509116633
NFKB1#479035.488063424193840.006049381815655430.0270030938772166
PAX5#507936.669565531177830.003370290999677260.0173197766921859
PBX3#5090321.91451268674419.49854535978121e-050.00136867905467741
POU2F2#545239.106124057742520.001324165192682130.0088338862062299
SIN3A#2594235.408884726815140.006318961977991520.0277334875617522
SPI1#668838.204323508522730.001810593189410520.0109222285051028
TCF12#6938310.63446490218640.0008313523990202070.00630130003637937
ZBTB7A#5134137.35190930787590.002516255860282270.0140502163062457



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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