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Coexpression cluster:C448: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.313352,3.98289,0.628682,0.521108,0.0703126,0.996809,1.20288,0.502803,0.794056,0.444446,0.47055,0.717665,0.367887,0.218743,0.0696927,0.580599,0.401017,0.047482,0.663348,0.872425,0.303125,0.23024,0.506057,0.240266,2.40962,0.275879,0.154326,0.502604,0.0717257,0.130724,2.68545,0.432083,0.143261,0.620439,0.203464,0.59709,0.199614,0.999899,0.690898,0.231945,0.20178,0.817201,1.12427,0.0690079,0.172498,0.705024,0.64558,0.453623,1.99383,0.251047,0.781754,0.665516,0.518992,0.49846,0.635443,0.629339,0.0737435,1.09023,0.464131,1.71055,0.467239,1.88603,0.266076,0.985416,0.680025,0.349807,0.716956,1.06805,0.423263,0.911622,0.391938,1.20366,0.07836,0.633615,0.180425,1.95535,0.0510358,0.364079,0.420511,0.35946,0.417805,0.983468,0.242227,0.114193,0.586887,1.36821,0.407926,0.0441419,3.16172,1.1648,0.804514,0.562601,0.446434,0.348406,0.904303,0.165445,0.206847,0.483243,0.310601,3.36536,0.173754,0.441596,0.47839,0.404088,0.902569,0.463465,0.39086,1.16194,1.21728,0.226477,0.656334,0.475985,0.0876862,0.941583,0.759328,0.0535109,1.60754,0.85634,1.64407,0.154062,0.626054,0.305079,0.172748,0.25053,0.863933,0.956184,0.222409,0.450719,0.66511,1.04453,0.563221,1.39703,0.678365,0.248069,0.81669,0.240417,0.427436,0.503505,0.776656,1.61314,1.21607,0.741657,0.223644,0.480173,0.905716,1.06736,0.875921,1.45545,0.406714,1.85046,0.945887,1.67348,0.563563,0.0236935,0.648756,0.940968,0.294363,0.495466,0.115044,3.60653,1.754,0.547006,0.419845,0.331484,0.354946,0.241648,0.316503,0.225998,1.73919
|tfbs_overrepresentation_for_novel_motifs=0.313352,3.98289,0.628682,0.521108,0.0703126,0.996809,1.20288,0.502803,0.794056,0.444446,0.47055,0.717665,0.367887,0.218743,0.0696927,0.580599,0.401017,0.047482,0.663348,0.872425,0.303125,0.23024,0.506057,0.240266,2.40962,0.275879,0.154326,0.502604,0.0717257,0.130724,2.68545,0.432083,0.143261,0.620439,0.203464,0.59709,0.199614,0.999899,0.690898,0.231945,0.20178,0.817201,1.12427,0.0690079,0.172498,0.705024,0.64558,0.453623,1.99383,0.251047,0.781754,0.665516,0.518992,0.49846,0.635443,0.629339,0.0737435,1.09023,0.464131,1.71055,0.467239,1.88603,0.266076,0.985416,0.680025,0.349807,0.716956,1.06805,0.423263,0.911622,0.391938,1.20366,0.07836,0.633615,0.180425,1.95535,0.0510358,0.364079,0.420511,0.35946,0.417805,0.983468,0.242227,0.114193,0.586887,1.36821,0.407926,0.0441419,3.16172,1.1648,0.804514,0.562601,0.446434,0.348406,0.904303,0.165445,0.206847,0.483243,0.310601,3.36536,0.173754,0.441596,0.47839,0.404088,0.902569,0.463465,0.39086,1.16194,1.21728,0.226477,0.656334,0.475985,0.0876862,0.941583,0.759328,0.0535109,1.60754,0.85634,1.64407,0.154062,0.626054,0.305079,0.172748,0.25053,0.863933,0.956184,0.222409,0.450719,0.66511,1.04453,0.563221,1.39703,0.678365,0.248069,0.81669,0.240417,0.427436,0.503505,0.776656,1.61314,1.21607,0.741657,0.223644,0.480173,0.905716,1.06736,0.875921,1.45545,0.406714,1.85046,0.945887,1.67348,0.563563,0.0236935,0.648756,0.940968,0.294363,0.495466,0.115044,3.60653,1.754,0.547006,0.419845,0.331484,0.354946,0.241648,0.316503,0.225998,1.73919
|tfbs_overrepresentation_jaspar=MA0003.1;4.91747,MA0004.1;0.158412,MA0006.1;0.895237,MA0007.1;0.146569,MA0009.1;0.526253,MA0014.1;0.441263,MA0017.1;0.0884918,MA0019.1;0.262545,MA0024.1;0.434294,MA0025.1;0.647545,MA0027.1;2.09389,MA0028.1;0.265828,MA0029.1;0.450974,MA0030.1;0.441064,MA0031.1;0.386141,MA0038.1;0.22896,MA0040.1;0.456051,MA0041.1;0.170492,MA0042.1;0.457543,MA0043.1;0.526535,MA0046.1;0.516541,MA0048.1;1.79118,MA0050.1;0.150446,MA0051.1;0.22589,MA0052.1;0.459414,MA0055.1;0.311622,MA0056.1;0,MA0057.1;0.0785329,MA0058.1;0.101748,MA0059.1;0.331581,MA0060.1;0.496174,MA0061.1;3.35522,MA0063.1;0,MA0066.1;0.649177,MA0067.1;0.820123,MA0068.1;2.83772,MA0069.1;0.51311,MA0070.1;0.503171,MA0071.1;0.201311,MA0072.1;0.499187,MA0073.1;0.330975,MA0074.1;0.639966,MA0076.1;0.110503,MA0077.1;0.49237,MA0078.1;0.30111,MA0081.1;0.331815,MA0083.1;0.532971,MA0084.1;0.999884,MA0087.1;0.497023,MA0088.1;0.61755,MA0089.1;0,MA0090.1;0.118716,MA0091.1;0.160096,MA0092.1;0.4236,MA0093.1;0.0708814,MA0095.1;0,MA0098.1;0,MA0100.1;0.672223,MA0101.1;1.37711,MA0103.1;0.501795,MA0105.1;2.81149,MA0106.1;0.259598,MA0107.1;5.84077,MA0108.2;0.383574,MA0109.1;0,MA0111.1;0.794681,MA0113.1;0.272101,MA0114.1;0.0401034,MA0115.1;0.747865,MA0116.1;0.672581,MA0117.1;0.560027,MA0119.1;0.308642,MA0122.1;0.583485,MA0124.1;0.70896,MA0125.1;0.631059,MA0130.1;0,MA0131.1;0.315517,MA0132.1;0,MA0133.1;0,MA0135.1;0.553498,MA0136.1;0.660517,MA0139.1;2.1546,MA0140.1;0.199454,MA0141.1;0.100114,MA0142.1;0.359701,MA0143.1;0.272236,MA0144.1;0.0352516,MA0145.1;4.1299,MA0146.1;0.998084,MA0147.1;1.50005,MA0148.1;0.518828,MA0149.1;0.192747,MA0062.2;0.204837,MA0035.2;0.198962,MA0039.2;0.741522,MA0138.2;0.302079,MA0002.2;0.0984982,MA0137.2;0.0801516,MA0104.2;1.15361,MA0047.2;0.698519,MA0112.2;0.45088,MA0065.2;0.0401599,MA0150.1;0.115337,MA0151.1;0,MA0152.1;0.20405,MA0153.1;0.615584,MA0154.1;1.54645,MA0155.1;0.609284,MA0156.1;0.58361,MA0157.1;0.337287,MA0158.1;0,MA0159.1;0.686643,MA0160.1;0.18494,MA0161.1;0,MA0162.1;0.692197,MA0163.1;1.46817,MA0164.1;0.770204,MA0080.2;1.36161,MA0018.2;2.86061,MA0099.2;0.204301,MA0079.2;0.151609,MA0102.2;1.03595,MA0258.1;0.032189,MA0259.1;1.09854,MA0442.1;0
}}
}}

Revision as of 19:10, 22 January 2013


Full id: C448_Eosinophils_CD19_Neutrophils_immature_CD14_CD34_CD4



Phase1 CAGE Peaks

Hg19::chr11:64619474..64619518,+p@chr11:64619474..64619518
+
Hg19::chr13:25861327..25861345,-p@chr13:25861327..25861345
-
Hg19::chr13:25861383..25861392,-p8@MTMR6
Hg19::chr13:25861424..25861442,-p3@MTMR6
Hg19::chr13:25861448..25861459,-p6@MTMR6
Hg19::chr13:25861474..25861481,-p5@MTMR6
Hg19::chr13:25861499..25861517,-p2@MTMR6
Hg19::chr15:55611198..55611219,+p5@PIGB
Hg19::chr17:3817800..3817817,+p@chr17:3817800..3817817
+
Hg19::chr19:18112074..18112107,+p4@ARRDC2
Hg19::chr19:18112109..18112115,+p10@ARRDC2
Hg19::chr1:172502624..172502648,-p1@BC034700
Hg19::chr21:43934531..43934564,-p@chr21:43934531..43934564
-
Hg19::chr22:50354104..50354157,+p2@PIM3
Hg19::chr22:50628844..50628860,-p@chr22:50628844..50628860
-
Hg19::chr2:158326065..158326081,-p@chr2:158326065..158326081
-
Hg19::chr3:42054612..42054635,+p@chr3:42054612..42054635
+
Hg19::chr6:30294289..30294313,+p2@TRIM39
Hg19::chr6:33378569..33378612,+p4@PHF1
Hg19::chr8:141608042..141608073,+p1@BC078139
Hg19::chr9:88356530..88356542,+p@chr9:88356530..88356542
+
Hg19::chrX:38186665..38186679,-p8@RPGR


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
leukocyte1.64e-86136
hematopoietic stem cell5.47e-73168
angioblastic mesenchymal cell5.47e-73168
hematopoietic cell7.02e-69177
nongranular leukocyte7.25e-67115
hematopoietic oligopotent progenitor cell3.27e-66161
hematopoietic multipotent progenitor cell3.27e-66161
hematopoietic lineage restricted progenitor cell4.21e-66120
classical monocyte4.79e-4642
CD14-positive, CD16-negative classical monocyte4.79e-4642
myeloid leukocyte6.19e-4572
granulocyte monocyte progenitor cell2.05e-3867
defensive cell2.36e-3848
phagocyte2.36e-3848
myeloid cell1.31e-34108
common myeloid progenitor1.31e-34108
macrophage dendritic cell progenitor1.41e-3461
myeloid lineage restricted progenitor cell1.77e-3366
monopoietic cell2.63e-3259
monocyte2.63e-3259
monoblast2.63e-3259
promonocyte2.63e-3259
lymphocyte1.25e-2853
common lymphoid progenitor1.25e-2853
lymphoid lineage restricted progenitor cell7.81e-2852
nucleate cell4.39e-2755
lymphocyte of B lineage1.69e-1824
pro-B cell1.69e-1824
mesenchymal cell3.90e-18354
B cell1.79e-1714
connective tissue cell3.59e-17361
stuff accumulating cell8.06e-1587
motile cell7.92e-14386
granulocyte3.50e-128
intermediate monocyte4.49e-129
CD14-positive, CD16-positive monocyte4.49e-129
stem cell3.80e-10441
multi fate stem cell6.80e-10427
somatic stem cell2.28e-09433
CD4-positive, alpha-beta T cell3.48e-096
mature alpha-beta T cell9.27e-0918
alpha-beta T cell9.27e-0918
immature T cell9.27e-0918
mature T cell9.27e-0918
immature alpha-beta T cell9.27e-0918
T cell2.71e-0825
pro-T cell2.71e-0825
blood cell3.02e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.00e-4398
blood island4.00e-4398
hemolymphoid system2.18e-38108
bone marrow8.38e-3576
immune system8.94e-3493
bone element6.00e-3182
skeletal element1.24e-2690
skeletal system2.99e-22100
connective tissue7.25e-16371
lateral plate mesoderm2.56e-11203
musculoskeletal system9.61e-08167


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)
MA0003.14.91747
MA0004.10.158412
MA0006.10.895237
MA0007.10.146569
MA0009.10.526253
MA0014.10.441263
MA0017.10.0884918
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.265828
MA0029.10.450974
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.10.170492
MA0042.10.457543
MA0043.10.526535
MA0046.10.516541
MA0048.11.79118
MA0050.10.150446
MA0051.10.22589
MA0052.10.459414
MA0055.10.311622
MA0056.10
MA0057.10.0785329
MA0058.10.101748
MA0059.10.331581
MA0060.10.496174
MA0061.13.35522
MA0063.10
MA0066.10.649177
MA0067.10.820123
MA0068.12.83772
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.10.330975
MA0074.10.639966
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.10.331815
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.61755
MA0089.10
MA0090.10.118716
MA0091.10.160096
MA0092.10.4236
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.672223
MA0101.11.37711
MA0103.10.501795
MA0105.12.81149
MA0106.10.259598
MA0107.15.84077
MA0108.20.383574
MA0109.10
MA0111.10.794681
MA0113.10.272101
MA0114.10.0401034
MA0115.10.747865
MA0116.10.672581
MA0117.10.560027
MA0119.10.308642
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.10.660517
MA0139.12.1546
MA0140.10.199454
MA0141.10.100114
MA0142.10.359701
MA0143.10.272236
MA0144.10.0352516
MA0145.14.1299
MA0146.10.998084
MA0147.11.50005
MA0148.10.518828
MA0149.10.192747
MA0062.20.204837
MA0035.20.198962
MA0039.20.741522
MA0138.20.302079
MA0002.20.0984982
MA0137.20.0801516
MA0104.21.15361
MA0047.20.698519
MA0112.20.45088
MA0065.20.0401599
MA0150.10.115337
MA0151.10
MA0152.10.20405
MA0153.10.615584
MA0154.11.54645
MA0155.10.609284
MA0156.10.58361
MA0157.10.337287
MA0158.10
MA0159.10.686643
MA0160.10.18494
MA0161.10
MA0162.10.692197
MA0163.11.46817
MA0164.10.770204
MA0080.21.36161
MA0018.22.86061
MA0099.20.204301
MA0079.20.151609
MA0102.21.03595
MA0258.10.032189
MA0259.11.09854
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
CCNT2#905133.744119113659744.52148768906304e-060.00014138312956828
CHD2#110694.231645704865990.000113058509480530.00154916264387787
CTCF#10664112.680128186537510.0008685684342533290.00648038424810569
CTCFL#140690108.975670163170164.06420961939136e-082.68137705899946e-06
E2F1#1869132.899820899701427.94249971490149e-050.00121646389166241
E2F6#1876132.964682932366646.23302721693576e-050.00102081092913526
EBF1#1879156.072591031751594.43514475306916e-104.33304099967999e-08
EGR1#1958153.401031201006911.35216734815753e-065.32098740294742e-05
ELF1#1997142.709698701059346.92225188485253e-050.00109921402554677
ELK4#200575.165898709512550.0002509219292283070.00270388313729623
ETS1#211373.095514838882560.005114965700967340.0237835315811107
HEY1#23462132.387338343653370.0006313022577310590.00518419378008917
HMGN3#932493.345769523188880.0006755108910917370.00545037715966702
MAX#4149133.812873709867853.66862353649845e-060.000120373035981263
MYC#4609143.323270281933265.92563771949817e-060.000177784452107633
NFKB1#4790153.741861425586713.73038743635991e-071.83340203983996e-05
NRF1#4899105.550127021686773.47417705175917e-060.000115701395761695
PAX5#5079133.94110690478692.50523996824564e-068.82146854496312e-05
POLR2A#5430222.147453176558074.97800844931664e-083.19544083858746e-06
RAD21#588573.294783512190650.003605583472029610.0182523160406815
REST#5978104.38637668914912.82986167844788e-050.000596945917663944
SIN3A#25942143.442017553427813.84586327170977e-060.000125557397384838
SMC3#912674.787024087024090.0004000926554224890.00390626127322327
SPI1#6688124.475085550103312.11279115254993e-067.6991554494474e-05
TAF1#6872182.735219688337067.10005359864782e-073.17840762018508e-05
TBP#6908162.695833226979191.01813841677941e-050.000266767080055256
TCF12#6938115.317232451093211.33198496006276e-065.24947838656585e-05
TCF7L2#693483.916427841140850.0005334871023112230.00461155930129795
YY1#7528112.455585374926930.001852671170780720.010933555088725
ZEB1#693596.908904007177032.1839493953915e-067.83543424614541e-05
ZNF143#770284.90940965535560.0001121509054876940.00154994421307785
ZNF263#10127103.737200744095760.0001131597360736970.00155034627781724



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:C448&oldid=2568959"