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Coexpression cluster:C1214: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.75236,0.384703,0.529489,0.90845,0.52784,0.604235,0.643217,0.637583,0.773341,0.497563,0.647852,1.03506,0.592674,0.341795,0.365029,0.827563,0.28906,1.08139,0.66776,0.384762,0.85713,0.520063,0.338096,0.430372,0.670692,0.957451,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.546594,0.8321,0.442372,0.305874,0.529001,0.282922,0.597792,0.307642,0.459366,0.0729319,0.340293,0.109128,1.06715,1.47235,1.22101,1.3209,0.915545,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.971313,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.131619,0.322252,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.194299,0.924148,1.70279,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.433733,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,0.722945,0.345641,0.241704,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,1.04428,0.7715,0.624608,0.695791,0.602897,0.033943
|tfbs_overrepresentation_for_novel_motifs=0.392069,0.75236,0.384703,0.529489,0.90845,0.52784,0.604235,0.643217,0.637583,0.773341,0.497563,0.647852,1.03506,0.592674,0.341795,0.365029,0.827563,0.28906,1.08139,0.66776,0.384762,0.85713,0.520063,0.338096,0.430372,0.670692,0.957451,0.517892,0.346214,0.150685,0.475674,0.864517,0.257226,0.546594,0.8321,0.442372,0.305874,0.529001,0.282922,0.597792,0.307642,0.459366,0.0729319,0.340293,0.109128,1.06715,1.47235,1.22101,1.3209,0.915545,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.638689,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,0.232216,0.115253,1.0929,0.179863,0.971313,0.156354,0.782748,0.850825,0.424224,0.200147,0.798651,0.625403,0.229431,1.04131,0.131619,0.322252,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,0.73028,0.343884,0.277058,0.194299,0.924148,1.70279,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.304323,0.155979,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,0.47854,1.14174,0.633392,1.28996,0.433733,0.469685,0.518459,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,0.722945,0.345641,0.241704,1.0153,0.619774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,1.04428,0.7715,0.624608,0.695791,0.602897,0.033943
|tfbs_overrepresentation_jaspar=MA0003.1;0.110456,MA0004.1;0.502801,MA0006.1;0.341337,MA0007.1;0.483857,MA0009.1;0.973289,MA0014.1;0.0156227,MA0017.1;0.380797,MA0019.1;0.652951,MA0024.1;0.867125,MA0025.1;1.10816,MA0027.1;2.59001,MA0028.1;0.35747,MA0029.1;0.886702,MA0030.1;0.875089,MA0031.1;0.809638,MA0038.1;0.60704,MA0040.1;0.892629,MA0041.1;0.521615,MA0042.1;0.48922,MA0043.1;0.973609,MA0046.1;0.962263,MA0048.1;0.766755,MA0050.1;0.490116,MA0051.1;0.602745,MA0052.1;0.896548,MA0055.1;0.158296,MA0056.1;0,MA0057.1;1.22064,MA0058.1;0.406232,MA0059.1;0.404929,MA0060.1;0.224688,MA0061.1;1.71672,MA0063.1;0,MA0066.1;0.607474,MA0067.1;1.29359,MA0068.1;0.162298,MA0069.1;0.958358,MA0070.1;0.947018,MA0071.1;0.567661,MA0072.1;0.942461,MA0073.1;0.00958848,MA0074.1;0.60198,MA0076.1;0.422297,MA0077.1;0.934645,MA0078.1;0.703614,MA0081.1;1.04478,MA0083.1;0.980893,MA0084.1;1.48179,MA0087.1;0.939982,MA0088.1;0.0723293,MA0089.1;0,MA0090.1;1.95014,MA0091.1;1.26109,MA0092.1;0.467172,MA0093.1;0.344385,MA0095.1;0,MA0098.1;0,MA0100.1;0.621149,MA0101.1;0.918548,MA0103.1;0.88373,MA0105.1;0.695228,MA0106.1;1.56379,MA0107.1;0.752965,MA0108.2;0.806528,MA0109.1;0,MA0111.1;0.45062,MA0113.1;0.665691,MA0114.1;1.36091,MA0115.1;1.21667,MA0116.1;0.277571,MA0117.1;1.01134,MA0119.1;0.388712,MA0122.1;1.03753,MA0124.1;1.17486,MA0125.1;1.0901,MA0130.1;0,MA0131.1;0.722072,MA0132.1;0,MA0133.1;0,MA0135.1;1.00402,MA0136.1;0.614215,MA0139.1;1.04496,MA0140.1;0.564957,MA0141.1;0.403171,MA0142.1;0.777365,MA0143.1;0.66587,MA0144.1;0.708913,MA0145.1;0.276317,MA0146.1;0.828373,MA0147.1;0.281049,MA0148.1;0.528066,MA0149.1;0.555119,MA0062.2;0.563664,MA0035.2;0.564239,MA0039.2;0.403603,MA0138.2;0.704862,MA0002.2;1.15032,MA0137.2;0.36398,MA0104.2;0.223944,MA0047.2;0.636643,MA0112.2;0.944394,MA0065.2;0.591589,MA0150.1;1.10099,MA0151.1;0,MA0152.1;0.571637,MA0153.1;1.07307,MA0154.1;0.102476,MA0155.1;0.534073,MA0156.1;0.36627,MA0157.1;0.749547,MA0158.1;0,MA0159.1;0.281681,MA0160.1;0.543522,MA0161.1;0,MA0162.1;0.106355,MA0163.1;0.19677,MA0164.1;0.678332,MA0080.2;0.344472,MA0018.2;2.64985,MA0099.2;0.572,MA0079.2;0.945415,MA0102.2;1.51913,MA0258.1;0.687127,MA0259.1;0.289405,MA0442.1;0
}}
}}

Revision as of 19:46, 22 January 2013


Full id: C1214_Eosinophils_Natural_CD14_Basophils_Neutrophils_Mast_CD34



Phase1 CAGE Peaks

Hg19::chr15:94850232..94850237,+p@chr15:94850232..94850237
+
Hg19::chr19:13957417..13957455,-p@chr19:13957417..13957455
-
Hg19::chr19:13973090..13973103,-p@chr19:13973090..13973103
-
Hg19::chr19:39894772..39894785,+p@chr19:39894772..39894785
+
Hg19::chr20:35233898..35233903,-p@chr20:35233898..35233903
-
Hg19::chr2:137000368..137000372,-p@chr2:137000368..137000372
-
Hg19::chr2:28582698..28582710,+p@chr2:28582698..28582710
+


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><br>

Cell Type
Ontology termp-valuen
classical monocyte7.69e-9242
CD14-positive, CD16-negative classical monocyte7.69e-9242
defensive cell9.33e-7948
phagocyte9.33e-7948
myeloid leukocyte8.60e-7872
leukocyte1.98e-73136
granulocyte monocyte progenitor cell2.48e-6367
myeloid lineage restricted progenitor cell1.32e-6166
macrophage dendritic cell progenitor5.43e-6161
monopoietic cell1.86e-6059
monocyte1.86e-6059
monoblast1.86e-6059
promonocyte1.86e-6059
hematopoietic stem cell7.36e-60168
angioblastic mesenchymal cell7.36e-60168
nongranular leukocyte4.13e-58115
hematopoietic lineage restricted progenitor cell2.95e-57120
hematopoietic cell6.69e-56177
hematopoietic oligopotent progenitor cell2.30e-53161
hematopoietic multipotent progenitor cell2.30e-53161
myeloid cell3.77e-51108
common myeloid progenitor3.77e-51108
stuff accumulating cell8.36e-3887
mesenchymal cell1.39e-20354
intermediate monocyte7.16e-209
CD14-positive, CD16-positive monocyte7.16e-209
connective tissue cell7.90e-20361
motile cell3.57e-17386
granulocyte4.44e-158
multi fate stem cell6.12e-14427
stem cell1.32e-13441
somatic stem cell1.71e-13433
blood cell1.30e-1011
natural killer cell5.79e-093
pro-NK cell5.79e-093
basophil1.87e-083
single nucleate cell1.90e-073
mononuclear cell1.90e-073
mature alpha-beta T cell4.32e-0718
alpha-beta T cell4.32e-0718
immature T cell4.32e-0718
mature T cell4.32e-0718
immature alpha-beta T cell4.32e-0718
non-classical monocyte4.75e-073
CD14-low, CD16-positive monocyte4.75e-073
Uber Anatomy
Ontology termp-valuen
bone marrow4.76e-5776
bone element6.30e-5282
hematopoietic system1.15e-4798
blood island1.15e-4798
skeletal element3.73e-4690
immune system3.02e-4493
hemolymphoid system5.57e-42108
skeletal system3.10e-40100
musculoskeletal system6.20e-19167
connective tissue8.44e-19371
lateral plate mesoderm6.43e-17203
mesoderm1.87e-07315
mesoderm-derived structure1.87e-07315
presumptive mesoderm1.87e-07315


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)
MA0003.10.110456
MA0004.10.502801
MA0006.10.341337
MA0007.10.483857
MA0009.10.973289
MA0014.10.0156227
MA0017.10.380797
MA0019.10.652951
MA0024.10.867125
MA0025.11.10816
MA0027.12.59001
MA0028.10.35747
MA0029.10.886702
MA0030.10.875089
MA0031.10.809638
MA0038.10.60704
MA0040.10.892629
MA0041.10.521615
MA0042.10.48922
MA0043.10.973609
MA0046.10.962263
MA0048.10.766755
MA0050.10.490116
MA0051.10.602745
MA0052.10.896548
MA0055.10.158296
MA0056.10
MA0057.11.22064
MA0058.10.406232
MA0059.10.404929
MA0060.10.224688
MA0061.11.71672
MA0063.10
MA0066.10.607474
MA0067.11.29359
MA0068.10.162298
MA0069.10.958358
MA0070.10.947018
MA0071.10.567661
MA0072.10.942461
MA0073.10.00958848
MA0074.10.60198
MA0076.10.422297
MA0077.10.934645
MA0078.10.703614
MA0081.11.04478
MA0083.10.980893
MA0084.11.48179
MA0087.10.939982
MA0088.10.0723293
MA0089.10
MA0090.11.95014
MA0091.11.26109
MA0092.10.467172
MA0093.10.344385
MA0095.10
MA0098.10
MA0100.10.621149
MA0101.10.918548
MA0103.10.88373
MA0105.10.695228
MA0106.11.56379
MA0107.10.752965
MA0108.20.806528
MA0109.10
MA0111.10.45062
MA0113.10.665691
MA0114.11.36091
MA0115.11.21667
MA0116.10.277571
MA0117.11.01134
MA0119.10.388712
MA0122.11.03753
MA0124.11.17486
MA0125.11.0901
MA0130.10
MA0131.10.722072
MA0132.10
MA0133.10
MA0135.11.00402
MA0136.10.614215
MA0139.11.04496
MA0140.10.564957
MA0141.10.403171
MA0142.10.777365
MA0143.10.66587
MA0144.10.708913
MA0145.10.276317
MA0146.10.828373
MA0147.10.281049
MA0148.10.528066
MA0149.10.555119
MA0062.20.563664
MA0035.20.564239
MA0039.20.403603
MA0138.20.704862
MA0002.21.15032
MA0137.20.36398
MA0104.20.223944
MA0047.20.636643
MA0112.20.944394
MA0065.20.591589
MA0150.11.10099
MA0151.10
MA0152.10.571637
MA0153.11.07307
MA0154.10.102476
MA0155.10.534073
MA0156.10.36627
MA0157.10.749547
MA0158.10
MA0159.10.281681
MA0160.10.543522
MA0161.10
MA0162.10.106355
MA0163.10.19677
MA0164.10.678332
MA0080.20.344472
MA0018.22.64985
MA0099.20.572
MA0079.20.945415
MA0102.21.51913
MA0258.10.687127
MA0259.10.289405
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
BCL11A#53335312.15833790154590.001376980163459870.00897077108674352
BCL3#602314.80590120160210.0007772745735585960.00609076974699026
CCNT2#90554.525858269259020.00155157330626470.00985613798023105
EP300#203343.870823843556110.01142567586684480.0418608770735073
FOS#235345.141688747939660.004042095865678250.019348815203757
FOSL2#235537.255800259097870.006020775093849750.0269861263476492
HMGN3#932444.673455841914620.005751881099938870.0259098861417518
JUN#372547.150188109906480.001171328177707770.00795864573232855
JUNB#3726313.11884256849480.00110478999316960.00767838970497372
MEF2C#4208211.80324414074970.01134538181234960.0416002644068385
NFKB1#479053.92004530299560.003036581424484610.0161196262779174
PAX5#507954.763975379412740.001218821047007470.00820077640306745
POU2F2#545245.203499461567160.003866714310179810.0190659447543019
SP1#666754.070272412957780.002549206128991580.0141112280121774
SPI1#668844.688184862012990.005685680529144170.0256670321496991
SRF#672235.913076398071920.01066868130167450.0393942301819257
TCF12#693857.596046358704590.0001311126373938080.00172459354367404
TCF7L2#693446.154386607507050.002064676148138040.01197227873163
ZEB1#693537.237899436090220.00606280792035710.02683364819232



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1214&oldid=2569725"