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Coexpression cluster:C870: Difference between revisions

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{{Coexpression_clusters
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regulation of I-kappaB kinase/NF-kappaB 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0.033888,0.368078,0.474502,0.576606,0.309128,0.533737,0.571519,0.434445,0.488829,0.363467,0.482434,0.561852,0.399782,0.343945,0.589766,0.530537,0.111066,0.44213,0.263525,0.148007,0.102613,0.628217,0.522084,0.226979,0.491955,0.287253,0.152349,0.152802,0.38832,0.216263,0.117262,0.152699,0.321649,0.231294,0.50945,0.129789,0.549887,0.132054,0.22458,0.266409,0.180355,0.322962,0.179632,0.282128,0.186072,0.0241955,0.338622,0.29306,0.00837228,0.187708,0.245457,0.106235,0.352719,0.496388,0.650742,0.269216,0.721601,0.0778925,0.599943,0.588096,0.0305736,0.538989,0.654598,0.584019,0.11758,0.0804409,0.235306,0.345488,0.408688,0.499886,0.486539,0.637365,0.554869,0.692656,0.308763,0.169082,0.0418662,0.307503,0.138853,0.13384,0.261561,0.0189238,0.0568823,0.41706,0.533176,0.255282,0.696023,0.179608,0.502814,0.0374633,0.236266,0.316751,0.431685,0.404852,0.613018,0.198522,0.611947,0.273479,0.530083,0.44039,0.401506,0.517565,0.0586842,0.0331568,0.739615|tfbs_overrepresentation_for_novel_motifs=0.83884,0.479568,0.305225,0.440628,0.737182,0.439064,0.511871,0.164003,0.487494,0.119197,0.410439,0.553754,0.40163,0.500805,0.266007,0.287179,0.728104,0.218596,0.426514,0.0599474,0.305279,0.141777,0.431698,0.726652,0.347482,0.575764,0.36063,0.429643,0.74357,0.10044,0.389837,0.764231,0.557092,0.406122,0.23642,0.261421,0.233607,0.440165,0.213144,0.14756,0.663028,0.374544,0.366128,0.264644,0.149259,0.887061,0.51292,0.4002,0.147122,0.270138,0.589559,0.524278,0.257164,0.839846,0.99088,0.503626,0.273964,0.472204,0.329728,0.47124,0.804523,0.5152,0.162346,0.700946,0.532513,0.667267,1.07848,1.44489,0.754027,1.28328,0.362234,0.168734,0.253077,0.988898,1.27856,0.114787,0.342172,0.684401,0.750836,0.341765,0.141333,0.699894,0.532172,0.166331,0.937974,0.358653,0.214403,0.096982,0.614883,1.54397,1.17124,0.911274,0.78075,1.08517,0.267904,0.207949,0.423564,0.82268,1.50181,0.0858425,0.613956,0.775192,0.817185,0.731699,0.656016,0.406162,0.716172,1.24409,0.347247,0.704291,0.315525,0.814459,0.300169,0.41935,1.12352,0.232218,0.685543,0.388709,0.664981,0.199081,0.980696,0.612519,0.436445,0.543065,1.23356,0.685145,0.50576,0.785662,1.02292,0.208774,0.911957,0.39253,1.03718,0.539846,1.18405,0.0922077,0.384215,0.430179,1.14186,1.99816,1.59626,1.10478,0.507423,0.819206,0.657732,0.464114,0.641461,1.83907,0.37143,0.565137,0.50389,0.347165,0.912334,0.155464,1.28086,1.31376,0.599133,0.708413,0.347536,0.320853,1.10357,0.894035,0.750062,0.323817,0.673453,0.531409,0.183544,0.510589,1.61842|tfbs_overrepresentation_jaspar=MA0003.1;0.605294,MA0004.1;0.415381,MA0006.1;0.265592,MA0007.1;0.397529,MA0009.1;0.870971,MA0014.1;0.205864,MA0017.1;0.301634,MA0019.1;0.558663,MA0024.1;0.766783,MA0025.1;1.00397,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;0.559235,MA0050.1;0.403421,MA0051.1;1.27173,MA0052.1;0.795605,MA0055.1;0.22215,MA0056.1;0,MA0057.1;0.253359,MA0058.1;0.325084,MA0059.1;0.323879,MA0060.1;0.162248,MA0061.1;0.432181,MA0063.1;0,MA0066.1;0.514973,MA0067.1;1.18766,MA0068.1;0.109867,MA0069.1;0.856287,MA0070.1;0.845142,MA0071.1;0.47692,MA0072.1;0.840664,MA0073.1;0.0776172,MA0074.1;0.509711,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;0.158781,MA0089.1;0,MA0090.1;0.353576,MA0091.1;1.07263,MA0092.1;0.381858,MA0093.1;0.26836,MA0095.1;0,MA0098.1;0,MA0100.1;0.528088,MA0101.1;1.36936,MA0103.1;0.257174,MA0105.1;0.496814,MA0106.1;0.554855,MA0107.1;1.75554,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;0.83188,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;0.406919,MA0140.1;0.474342,MA0141.1;0.861836,MA0142.1;0.679161,MA0143.1;0.571113,MA0144.1;0.1885,MA0145.1;0.706237,MA0146.1;0.51271,MA0147.1;0.211483,MA0148.1;0.439278,MA0149.1;0.464973,MA0062.2;0.135498,MA0035.2;0.473658,MA0039.2;0.109483,MA0138.2;0.608783,MA0002.2;0.152495,MA0137.2;0.28622,MA0104.2;0.161609,MA0047.2;0.542971,MA0112.2;0.378721,MA0065.2;0.182082,MA0150.1;0.919271,MA0151.1;0,MA0152.1;1.20819,MA0153.1;0.969315,MA0154.1;0.488402,MA0155.1;0.359913,MA0156.1;0.288314,MA0157.1;0.652111,MA0158.1;0,MA0159.1;0.212043,MA0160.1;1.15068,MA0161.1;0,MA0162.1;0.0533066,MA0163.1;0.216998,MA0164.1;0.583138,MA0080.2;0.268439,MA0018.2;0.556211,MA0099.2;0.481058,MA0079.2;0.214283,MA0102.2;1.41188,MA0258.1;0.180288,MA0259.1;0.218904,MA0442.1;0}}
|full_id=C870_CD14_Mast_Basophils_Peripheral_Eosinophils_Endothelial_Natural
|id=C870
}}

Latest revision as of 11:32, 17 September 2013


Full id: C870_CD14_Mast_Basophils_Peripheral_Eosinophils_Endothelial_Natural



Phase1 CAGE Peaks

Hg19::chr10:17010725..17010731,-p@chr10:17010725..17010731
-
Hg19::chr11:93256270..93256311,+p@chr11:93256270..93256311
+
Hg19::chr19:13953553..13953571,+p@chr19:13953553..13953571
+
Hg19::chr4:139937826..139937827,+p@chr4:139937826..139937827
+
Hg19::chr4:140656102..140656142,-p@chr4:140656102..140656142
-
Hg19::chr4:140657557..140657602,-p@chr4:140657557..140657602
-
Hg19::chr4:40058783..40058795,-p3@LOC344967
Hg19::chr5:172194496..172194500,-p@chr5:172194496..172194500
-
Hg19::chr6:138192305..138192312,+p51@TNFAIP3


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:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0102437301306959



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
single nucleate cell6.54e-383
mononuclear cell6.54e-383
classical monocyte2.70e-3442
CD14-positive, CD16-negative classical monocyte2.70e-3442
defensive cell7.35e-3048
phagocyte7.35e-3048
monopoietic cell1.21e-2359
monocyte1.21e-2359
monoblast1.21e-2359
promonocyte1.21e-2359
myeloid leukocyte5.28e-2372
macrophage dendritic cell progenitor7.71e-2361
nongranular leukocyte2.27e-22115
leukocyte1.69e-21136
myeloid lineage restricted progenitor cell4.85e-2166
granulocyte monocyte progenitor cell1.03e-2067
circulating cell2.49e-196
hematopoietic stem cell4.19e-17168
angioblastic mesenchymal cell4.19e-17168
hematopoietic cell3.76e-16177
stuff accumulating cell6.64e-1687
myeloid cell6.27e-15108
common myeloid progenitor6.27e-15108
intermediate monocyte2.09e-139
CD14-positive, CD16-positive monocyte2.09e-139
hematopoietic lineage restricted progenitor cell2.74e-13120
hematopoietic oligopotent progenitor cell2.30e-11161
hematopoietic multipotent progenitor cell2.30e-11161
mesenchymal cell3.77e-07354
connective tissue cell5.67e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.69e-2398
blood island6.69e-2398
hemolymphoid system1.18e-20108
bone marrow3.85e-1876
bone element9.82e-1782
skeletal element3.80e-1590
immune system1.28e-1493
skeletal system1.64e-13100
lateral plate mesoderm3.10e-10203
blood4.43e-0815
haemolymphatic fluid4.43e-0815
organism substance4.43e-0815
musculoskeletal system1.47e-07167
connective tissue9.92e-07371


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)
MA0003.10.605294
MA0004.10.415381
MA0006.10.265592
MA0007.10.397529
MA0009.10.870971
MA0014.10.205864
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
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
MA0048.10.559235
MA0050.10.403421
MA0051.11.27173
MA0052.10.795605
MA0055.10.22215
MA0056.10
MA0057.10.253359
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.10.432181
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.0776172
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.11.07263
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.11.36936
MA0103.10.257174
MA0105.10.496814
MA0106.10.554855
MA0107.11.75554
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.599942
MA0117.10.908433
MA0119.10.83188
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.861836
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.706237
MA0146.10.51271
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.109483
MA0138.20.608783
MA0002.20.152495
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.378721
MA0065.20.182082
MA0150.10.919271
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.488402
MA0155.10.359913
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.212043
MA0160.11.15068
MA0161.10
MA0162.10.0533066
MA0163.10.216998
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.214283
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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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