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Coexpression cluster:C865: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.383295,0.273994,0.404877,0.237701,1.04099,0.474413,0.434224,0.138703,0.437939,0.375531,0.515448,0.107365,1.17144,0.666154,0.256724,0.68716,0.191625,0.371758,0.178097,0.274046,0.503302,0.396189,1.22721,0.844704,0.537051,0.641011,0.39419,0.240354,0.590419,0.935963,0.722879,0.495657,0.108961,0.20845,1.1313,0.20579,0.404426,0.186493,0.395523,0.597291,0.340749,0.302519,0.235234,0.0391382,0.301189,0.47544,0.365597,0.518466,0.240465,0.550604,1.22072,0.812657,0.797754,0.947672,0.466348,0.244111,1.11117,0.994052,0.434711,0.762758,0.477672,0.430344,0.660336,0.494624,0.627106,1.0348,1.4,0.712787,1.2388,0.328852,0.445273,0.210881,0.945703,0.104203,0.0955465,0.292851,0.644006,2.8385,2.29502,1.24887,0.659298,0.49429,0.864635,0.89511,0.0102458,3.85608,0.0795497,0.575506,1.4989,1.12715,0.868602,0.739223,0.982336,0.238337,3.06772,0.743843,0.780743,0.579925,2.45119,0.550108,0.733724,1.82585,0.690713,0.616014,0.37138,0.675372,0.460348,0.31439,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.204477,0.0648813,0.354459,0.624851,0.173291,0.937551,0.57318,0.400807,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.537508,0.869279,0.358161,0.993705,2.16696,2.57009,0.553614,0.350108,0.394712,1.09788,1.95265,1.55112,1.06096,2.06144,1.82998,0.617705,0.42776,0.601672,1.79367,0.337738,0.971618,0.052013,0.0287097,0.869654,0.414185,1.2007,1.26919,0.560015,0.64107,0.314669,0.786832,1.05976,0.851493,0.708865,0.291837,0.633206,0.493542,0.158769,2.07178,0.393553
|tfbs_overrepresentation_jaspar=MA0003.1;0.1987,MA0004.1;0.990587,MA0006.1;0.665232,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.15363,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.697761,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;0.817858,MA0048.1;0.0613414,MA0050.1;0.368721,MA0051.1;0.473017,MA0052.1;0.753928,MA0055.1;0.0662377,MA0056.1;0,MA0057.1;2.85487,MA0058.1;0.293055,MA0059.1;0.291897,MA0060.1;0.430116,MA0061.1;0.757837,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;1.05557,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;0.0447366,MA0074.1;2.06891,MA0076.1;0.307383,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;1.44489,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.0309101,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.671378,MA0095.1;0,MA0098.1;0,MA0100.1;0.49029,MA0101.1;1.25862,MA0103.1;0.646502,MA0105.1;0.422512,MA0106.1;0.516528,MA0107.1;1.01551,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;2.26745,MA0114.1;0.174997,MA0115.1;1.06753,MA0116.1;0.182037,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;0.109245,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;0.163394,MA0145.1;0.332712,MA0146.1;0.4029,MA0147.1;0.543675,MA0148.1;0.403564,MA0149.1;1.09589,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.233545,MA0138.2;1.39695,MA0002.2;0.80943,MA0137.2;0.255808,MA0104.2;0.428616,MA0047.2;0.504873,MA0112.2;0.0329985,MA0065.2;0.147044,MA0150.1;1.52802,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;0.185581,MA0155.1;0.12484,MA0156.1;0.715501,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.544949,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.108522,MA0163.1;0.0235237,MA0164.1;0.544294,MA0080.2;0.671553,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;1.79688,MA0102.2;1.36707,MA0258.1;0.155735,MA0259.1;1.06648,MA0442.1;0
}}
}}

Revision as of 19:30, 22 January 2013


Full id: C865_CD14_Neutrophils_Dendritic_placenta_cervical_epitheloid_spinal



Phase1 CAGE Peaks

Hg19::chrX:1367460..1367489,+p@chrX:1367460..1367489
+
Hg19::chrX:1368516..1368527,-p@chrX:1368516..1368527
-
Hg19::chrX:1387700..1387717,+p1@CSF2RA
Hg19::chrX:1387721..1387738,+p2@CSF2RA
Hg19::chrX:1393727..1393755,-p@chrX:1393727..1393755
-
Hg19::chrX:1393820..1393849,-p@chrX:1393820..1393849
-
Hg19::chrX:1435460..1435487,-p@chrX:1435460..1435487
-
Hg19::chrX:1435588..1435602,-p@chrX:1435588..1435602
-
Hg19::chrX:1455478..1455515,+p2@IL3RA
Hg19::chrX:24167737..24167762,-p1@ZFX-AS1


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
8.58567593366187e-050.01358683216501992265Cytokine-cytokine receptor interaction (KEGG):04060
2.92938943019595e-050.006181011697713452155Jak-STAT signaling pathway (KEGG):04630
9.39564536136585e-060.00297372175687229288Hematopoietic cell lineage (KEGG):04640
0.0003198274735665560.03374179846127162511Signaling in Immune system (Reactome):REACT_6900
1.91447319275479e-060.00121186153101378240IL-3 up reg. targets (Netpath):NetPath_15
0.0002017928378747890.02554697327494832406{GRB2,414} (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

GO IDGO nameFDR corrected p-value
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.000158559827157831
GO:0004912interleukin-3 receptor activity0.00153064978927681
GO:0019978interleukin-3 binding0.00153064978927681
GO:0004907interleukin receptor activity0.0183575242003379
GO:0019965interleukin binding0.0183575242003379
GO:0004888transmembrane receptor activity0.0230388577844583
GO:0019838growth factor binding0.028372121655368
GO:0019955cytokine binding0.028372121655368
GO:0004872receptor activity0.035793698202971
GO:0005057receptor signaling protein activity0.0387720512564269
GO:0004871signal transducer activity0.0387720512564269
GO:0060089molecular transducer activity0.0387720512564269



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
myeloid lineage restricted progenitor cell3.41e-3666
granulocyte monocyte progenitor cell1.47e-3567
myeloid leukocyte2.02e-3572
monopoietic cell3.39e-3259
monocyte3.39e-3259
monoblast3.39e-3259
promonocyte3.39e-3259
macrophage dendritic cell progenitor5.92e-3161
classical monocyte3.33e-3042
CD14-positive, CD16-negative classical monocyte3.33e-3042
defensive cell1.38e-2848
phagocyte1.38e-2848
myeloid cell5.87e-27108
common myeloid progenitor5.87e-27108
hematopoietic lineage restricted progenitor cell5.81e-17120
leukocyte5.88e-17136
hematopoietic stem cell6.63e-16168
angioblastic mesenchymal cell6.63e-16168
hematopoietic oligopotent progenitor cell1.28e-15161
hematopoietic multipotent progenitor cell1.28e-15161
stuff accumulating cell5.34e-1587
hematopoietic cell1.04e-14177
nongranular leukocyte1.09e-13115
histamine secreting cell3.77e-075
biogenic amine secreting cell3.77e-075
granulocytopoietic cell3.77e-075
mast cell3.77e-075
mast cell progenitor3.77e-075
basophil mast progenitor cell3.77e-075
Uber Anatomy
Ontology termp-valuen
bone marrow1.39e-3076
bone element7.21e-2882
immune system1.02e-2593
skeletal element8.27e-2590
hematopoietic system4.64e-2498
blood island4.64e-2498
skeletal system1.64e-23100
hemolymphoid system3.35e-21108
neural tube3.05e-1456
neural rod3.05e-1456
future spinal cord3.05e-1456
neural keel3.05e-1456
spinal cord8.34e-123
dorsal region element8.34e-123
dorsum8.34e-123
musculoskeletal system2.25e-11167
regional part of nervous system6.71e-1053
regional part of brain6.71e-1053
central nervous system8.59e-1081
regional part of telencephalon5.43e-0932
lateral plate mesoderm5.84e-09203
regional part of cerebral cortex1.01e-0822
neural plate1.36e-0882
presumptive neural plate1.36e-0882
nervous system1.89e-0889
brain grey matter2.25e-0834
gray matter2.25e-0834
telencephalon2.25e-0834
posterior neural tube2.90e-0815
chordal neural plate2.90e-0815
regional part of forebrain3.89e-0841
forebrain3.89e-0841
anterior neural tube3.89e-0841
future forebrain3.89e-0841
neurectoderm4.97e-0886
middle temporal gyrus5.26e-082
cerebral cortex1.42e-0725
pallium1.42e-0725
neocortex2.10e-0720
cerebral hemisphere2.98e-0732
brain5.57e-0768
future brain5.57e-0768


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)
MA0003.10.1987
MA0004.10.990587
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.15363
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.0613414
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.12.85487
MA0058.10.293055
MA0059.10.291897
MA0060.10.430116
MA0061.10.757837
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.11.05557
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.0447366
MA0074.12.06891
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.11.44489
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.671378
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.11.25862
MA0103.10.646502
MA0105.10.422512
MA0106.10.516528
MA0107.11.01551
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.12.26745
MA0114.10.174997
MA0115.11.06753
MA0116.10.182037
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
MA0139.10.109245
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.332712
MA0146.10.4029
MA0147.10.543675
MA0148.10.403564
MA0149.11.09589
MA0062.20.114378
MA0035.20.437071
MA0039.20.233545
MA0138.21.39695
MA0002.20.80943
MA0137.20.255808
MA0104.20.428616
MA0047.20.504873
MA0112.20.0329985
MA0065.20.147044
MA0150.11.52802
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.185581
MA0155.10.12484
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.544949
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.10.0235237
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.21.79688
MA0102.21.36707
MA0258.10.155735
MA0259.11.06648
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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