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Coexpression cluster:C813: Difference between revisions

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{{Coexpression_clusters
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activity!0.0453431196630803!2595$GO:0045843!negative regulation of striated muscle development!0.0453431196630803!9734$GO:0032488!Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0043088!regulation of Cdc42 GTPase activity!0.0453431196630803!221472$GO:0032489!regulation of Cdc42 protein signal transduction!0.0453431196630803!221472$GO:0032319!regulation of Rho GTPase activity!0.0453431196630803!221472$GO:0016202!regulation of striated muscle development!0.0453431196630803!9734$GO:0016566!specific transcriptional repressor activity!0.0453431196630803!9734$GO:0015926!glucosidase 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4002,0.454236,0.620409,0.470098,0.0773001,0.53945,0.587396,0.0293568,0.51191,0.0521442,0.568699,0.40594,0.351828,0.19831,0.521951,0.498061,0.355143,0.523646,0.10457,0.278571,0.35692,0.483693,0.212078,0.663478,0.257808,0.0808049,0.541075,0.0710305,0.205005,0.207337,0.183784,0.276486,0.329711,0.0978515,0.580521,0.118522,0.579662,0.459939,0.122652,0.203837,0.163644,0.143933,0.280163,0.173534,0.421304,0.109286,0.347441,0.292694,0.0569723,0.185106,0.195115,0.113787,0.563762,0.515166,0.357319,0.632866,0.706798,0.485196,0.115594,0.628986,0.41993,0.557752,0.356596,0.492927,0.495033,0.221402,0.630984,0.636345,0.532147,0.551524,0.539507,0.399497,0.161,0.0722036,0.33694,0.208477,0.610026,0.469149,0.525556,0.0907839,0.518957,0.233702,0.432878,0.373963,0.260574,0.568369,0.467238,0.477159,0.288135,0.52892,0.710278,0.300745,0.559725,0.248778,0.528779,0.313572,0.167775,0.0150255,0.0181309,0.237199,0.129411,0.0150049,0.723393,0.0824214,0.546774,0.499966,0.588091,0.503708,0.246187,0.0472547,0.198269,0.351675,0.0209275,0.308086,0.20448,0.232324,0.368317,0.319783,0.139615,0.206257,0.268704,0.117319,0.383259,0.177677,0.689269,0.104903,0.171545,0.399175,0.270842,0.626754,0.52491,0.576995,0.693079,0.622646,0.479007,0.305345,0.272931,0.0122817,0.44222,0.536945,0.17005,0.676017,0.593153,0.730416,0.336551,0.198375,0.0540508,0.0637855,0.514691,0.506629,0.100192,0.670422,0.249066,0.450988,0.571064,0.279276,0.148243,0.573814,0.182763,0.285349,0.2588,0.719228,0.46627,0.11426,0.65176,0.0257031,0.0900708,0.298817,0.567905,0.136936,0.434688,0.555097,0.621443,0.536392,0.775775|tfbs_overrepresentation_for_novel_motifs=0.280498,2.37683,0.273994,0.404877,0.237701,0.403356,0.474413,0.434224,0.847231,0.0209902,0.375531,0.515448,0.348369,0.46359,0.236531,0.256724,0.68716,0.191625,1.22644,0.708167,2.11869,0.805814,0.396189,0.233338,0.314616,0.537051,0.641011,0.39419,0.240354,0.0826403,0.355553,0.722879,0.165252,0.352585,0.600053,0.0928746,0.20579,0.404426,0.547451,0.789486,0.207288,0.340749,0.878641,0.235234,0.644296,0.814459,0.47544,0.365597,0.518466,1.2542,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,0.244111,0.435652,0.281305,0.434711,0.762758,0.477672,0.848838,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.210881,0.945703,0.339984,0.0955465,0.0867529,1.55336,0.709631,0.309107,0.380738,0.659298,0.49429,0.142768,0.89511,0.285658,0.175904,0.575051,0.575506,1.4989,1.12715,0.868602,0.739223,0.509773,0.670367,0.18161,0.368981,0.780743,0.579925,1.34829,1.04928,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.590599,0.0136871,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,1.18186,0.744085,0.979528,0.537508,0.869279,0.358161,0.993705,0.50181,1.13991,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.168379,0.193209,0.119096,0.869654,0.132719,0.477214,1.26919,1.37691,0.225815,0.314669,0.28899,1.05976,0.851493,0.708865,0.793294,0.633206,0.493542,0.158769,1.192,0.248237|tfbs_overrepresentation_jaspar=MA0003.1;1.07531,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.954641,MA0017.1;0.744788,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.25013,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;1.91352,MA0048.1;0.220931,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.344701,MA0056.1;0,MA0057.1;0.0580131,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.138988,MA0061.1;0.377096,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;0.000749839,MA0074.1;0.4723,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.79376,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.300184,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.995927,MA0092.1;0.347826,MA0093.1;0.671378,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;0.678051,MA0103.1;0.646502,MA0105.1;0.422512,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.998594,MA0115.1;2.42332,MA0116.1;0.536665,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;0.585907,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.716757,MA0140.1;1.95291,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.491079,MA0145.1;0.602634,MA0146.1;1.14011,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.366815,MA0035.2;0.437071,MA0039.2;0.936681,MA0138.2;0.569505,MA0002.2;1.90479,MA0137.2;0.255808,MA0104.2;0.428616,MA0047.2;0.504873,MA0112.2;0.573053,MA0065.2;1.37627,MA0150.1;0.315136,MA0151.1;0,MA0152.1;0.443956,MA0153.1;2.13564,MA0154.1;0.729959,MA0155.1;0.030416,MA0156.1;0.715501,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.185458,MA0160.1;1.07255,MA0161.1;0,MA0162.1;0.229496,MA0163.1;1.30834,MA0164.1;0.544294,MA0080.2;1.93598,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;0.0513543,MA0102.2;1.36707,MA0258.1;0.155735,MA0259.1;0.560522,MA0442.1;0}}
|full_id=C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma
|id=C813
}}

Latest revision as of 11:31, 17 September 2013


Full id: C813_CD19_CD14CD16_CD14_Macrophage_Monocytederived_pancreatic_choriocarcinoma



Phase1 CAGE Peaks

Hg19::chr12:109027413..109027428,-p@chr12:109027413..109027428
-
Hg19::chr15:42566384..42566475,+p2@GANC
Hg19::chr19:3178856..3178869,+p3@S1PR4
Hg19::chr1:198609269..198609281,+p@chr1:198609269..198609281
+
Hg19::chr3:46968478..46968499,-p@chr3:46968478..46968499
-
Hg19::chr4:164534657..164534701,-p1@MARCH1
Hg19::chr5:122110718..122110800,+p1@SNX2
Hg19::chr6:36973462..36973468,+p2@FGD2
Hg19::chr6:36973470..36973478,+p3@FGD2
Hg19::chr7:18330064..18330080,+p3@HDAC9


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:0004558alpha-glucosidase activity0.0453431196630803
GO:0045843negative regulation of striated muscle development0.0453431196630803
GO:0032488Cdc42 protein signal transduction0.0453431196630803
GO:0043088regulation of Cdc42 GTPase activity0.0453431196630803
GO:0032489regulation of Cdc42 protein signal transduction0.0453431196630803
GO:0032319regulation of Rho GTPase activity0.0453431196630803
GO:0016202regulation of striated muscle development0.0453431196630803
GO:0016566specific transcriptional repressor activity0.0453431196630803
GO:0015926glucosidase activity0.0453431196630803



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
leukocyte1.17e-72136
nongranular leukocyte1.01e-65115
hematopoietic stem cell1.19e-65168
angioblastic mesenchymal cell1.19e-65168
hematopoietic oligopotent progenitor cell9.34e-61161
hematopoietic multipotent progenitor cell9.34e-61161
hematopoietic lineage restricted progenitor cell1.94e-60120
hematopoietic cell6.63e-60177
macrophage dendritic cell progenitor2.58e-4961
monopoietic cell2.11e-4759
monocyte2.11e-4759
monoblast2.11e-4759
promonocyte2.11e-4759
granulocyte monocyte progenitor cell2.88e-4767
myeloid leukocyte5.82e-4772
myeloid lineage restricted progenitor cell1.94e-4266
myeloid cell3.82e-41108
common myeloid progenitor3.82e-41108
defensive cell4.54e-4148
phagocyte4.54e-4148
classical monocyte4.76e-3642
CD14-positive, CD16-negative classical monocyte4.76e-3642
lymphocyte of B lineage5.78e-2024
pro-B cell5.78e-2024
lymphocyte1.18e-1653
common lymphoid progenitor1.18e-1653
lymphoid lineage restricted progenitor cell4.61e-1652
nucleate cell1.49e-1555
B cell1.78e-1414
stuff accumulating cell3.32e-1487
dendritic cell3.52e-1110
intermediate monocyte2.44e-109
CD14-positive, CD16-positive monocyte2.44e-109
mesenchymal cell2.68e-10354
connective tissue cell1.84e-09361
conventional dendritic cell3.39e-098
immature conventional dendritic cell2.31e-075
common dendritic progenitor2.31e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.80e-5198
blood island4.80e-5198
hemolymphoid system1.54e-46108
bone marrow1.91e-4176
immune system1.74e-3893
bone element1.60e-3682
skeletal element4.97e-3190
skeletal system1.78e-26100
adult organism1.91e-24114
lateral plate mesoderm1.66e-14203
connective tissue1.07e-08371
musculoskeletal system1.07e-08167
blood1.81e-0815
haemolymphatic fluid1.81e-0815
organism substance1.81e-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)
MA0003.11.07531
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.954641
MA0017.10.744788
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.11.91352
MA0048.10.220931
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.344701
MA0056.10
MA0057.10.0580131
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.377096
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.000749839
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.79376
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.300184
MA0089.10
MA0090.10.320494
MA0091.10.995927
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.678051
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.12.42332
MA0116.10.536665
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.11.95291
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.491079
MA0145.10.602634
MA0146.11.14011
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.366815
MA0035.20.437071
MA0039.20.936681
MA0138.20.569505
MA0002.21.90479
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.20.573053
MA0065.21.37627
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.12.13564
MA0154.10.729959
MA0155.10.030416
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.11.07255
MA0161.10
MA0162.10.229496
MA0163.11.30834
MA0164.10.544294
MA0080.21.93598
MA0018.20.517858
MA0099.20.444294
MA0079.20.0513543
MA0102.21.36707
MA0258.10.155735
MA0259.10.560522
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
EBF1#187954.45323342328450.002759080257038690.0151278655483444
IRF4#366248.765805074697650.000728667835365060.00580970608883819
NFKB1#479063.29283805451630.00391275252059270.0190696700965132
SPI1#668864.922594105113640.0004434197902305250.00412858335311454
SRF#672245.518871304867120.004058059466626480.019413662802208



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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