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Coexpression cluster:C999: Difference between revisions

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{{Coexpression_clusters
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cleavage factor complex!0.00988864149387627!51585$GO:0044451!nucleoplasm part!0.00988864149387627!26512;51585$GO:0005654!nucleoplasm!0.00988864149387627!26512;51585$GO:0006379!mRNA cleavage!0.00988864149387627!51585$GO:0006396!RNA processing!0.00988864149387627!26512;51585$GO:0016073!snRNA metabolic process!0.00988864149387627!26512$GO:0016180!snRNA processing!0.00988864149387627!26512$GO:0032039!integrator complex!0.00988864149387627!26512$GO:0031981!nuclear lumen!0.00988864149387627!26512;51585$GO:0044446!intracellular organelle part!0.0119162554456562!26512;5770;51585$GO:0044422!organelle part!0.0119162554456562!26512;5770;51585$GO:0031974!membrane-enclosed lumen!0.0134872640129136!26512;51585$GO:0043233!organelle lumen!0.0134872640129136!26512;51585$GO:0008286!insulin receptor signaling pathway!0.0147213814335944!5770$GO:0044428!nuclear part!0.015180302815631!26512;51585$GO:0016591!DNA-directed RNA polymerase II, 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516,0.800646,1.33315,1.03556,0.197328,1.56216,1.03748,1.43212,0.846634,0.127753,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,0.19474,0.986227,1.47034,0.26222,0.118789,0.659621,1.59442,1.22073,0.959334,0.827657,0.227232,0.817658,0.672575,0.488357,0.87,0.664183,0.106284,0.246049,0.822041,0.864454,0.778061,0.701386,1.13403,0.762347,0.539961,1.00159,2.18389,0.352381,0.861701,0.336372,0.459808,1.17281,0.265019,0.279527,0.428232,0.710479,0.229841,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,0.240162,0.960022,0.432175,1.08604,0.583225,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,1.1925,0.0833399,2.1277,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,0.385642,0.941217,1.15277,0.941964,0.796636,0.36101,0.71907,0.574616,0.611402,0.553354,1.95084|tfbs_overrepresentation_jaspar=MA0003.1;3.24424,MA0004.1;1.15451,MA0006.1;0.812175,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;1.78293,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;1.05265,MA0027.1;2.5321,MA0028.1;0.846854,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.653157,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.283474,MA0056.1;0,MA0057.1;0.632427,MA0058.1;2.55421,MA0059.1;1.69011,MA0060.1;1.67203,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;0.823119,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.215282,MA0074.1;1.36092,MA0076.1;0.985027,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;0.926258,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.441522,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;3.13688,MA0095.1;0,MA0098.1;0,MA0100.1;1.40058,MA0101.1;0.825856,MA0103.1;0.291333,MA0105.1;0.586268,MA0106.1;1.45807,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;0.405141,MA0113.1;0.614917,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;1.60834,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;0.564434,MA0139.1;0.470675,MA0140.1;0.516266,MA0141.1;0.359385,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.218541,MA0145.1;0.480646,MA0146.1;1.63914,MA0147.1;1.26392,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;1.50503,MA0035.2;0.515566,MA0039.2;4.9691,MA0138.2;2.6595,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;1.66814,MA0047.2;0.586412,MA0112.2;0.208783,MA0065.2;0.226158,MA0150.1;1.00335,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;1.64163,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;2.66274,MA0163.1;0.493198,MA0164.1;0.627336,MA0080.2;0.303167,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;6.37808,MA0102.2;1.46209,MA0258.1;0.603127,MA0259.1;0.699589,MA0442.1;0}}
|full_id=C999_CD14_Eosinophils_Mast_Neutrophils_CD19_CD8_CD4
|gostat_on_coexpression_clusters=GO:0005849!mRNA cleavage factor complex!0.00988864149387627!51585$GO:0044451!nucleoplasm part!0.00988864149387627!26512;51585$GO:0005654!nucleoplasm!0.00988864149387627!26512;51585$GO:0006379!mRNA cleavage!0.00988864149387627!51585$GO:0006396!RNA processing!0.00988864149387627!26512;51585$GO:0016073!snRNA metabolic process!0.00988864149387627!26512$GO:0016180!snRNA processing!0.00988864149387627!26512$GO:0032039!integrator complex!0.00988864149387627!26512$GO:0031981!nuclear lumen!0.00988864149387627!26512;51585$GO:0044446!intracellular organelle part!0.0119162554456562!26512;5770;51585$GO:0044422!organelle part!0.0119162554456562!26512;5770;51585$GO:0031974!membrane-enclosed lumen!0.0134872640129136!26512;51585$GO:0043233!organelle lumen!0.0134872640129136!26512;51585$GO:0008286!insulin receptor signaling pathway!0.0147213814335944!5770$GO:0044428!nuclear part!0.015180302815631!26512;51585$GO:0016591!DNA-directed RNA polymerase II, holoenzyme!0.0461787976172104!26512
|id=C999
|ontology_enrichment_celltype=CL:0000037!1.56e-57!172;CL:0000566!1.56e-57!172;CL:0000738!8.93e-56!140;CL:0002032!1.52e-53!165;CL:0000837!1.52e-53!165;CL:0000988!5.49e-52!182;CL:0002031!4.66e-46!124;CL:0002087!5.62e-44!119;CL:0000763!1.14e-34!112;CL:0000049!1.14e-34!112;CL:0000766!1.06e-32!76;CL:0000557!2.69e-29!71;CL:0000839!5.76e-28!70;CL:0002057!1.87e-26!42;CL:0002009!2.31e-26!65;CL:0000860!3.34e-26!45;CL:0002194!2.26e-25!63;CL:0000576!2.26e-25!63;CL:0000040!2.26e-25!63;CL:0000559!2.26e-25!63;CL:0000542!3.21e-16!53;CL:0000051!3.21e-16!53;CL:0000838!4.63e-16!52;CL:0000791!5.86e-09!18;CL:0000789!5.86e-09!18;CL:0002420!5.86e-09!18;CL:0002419!5.86e-09!18;CL:0000790!5.86e-09!18;CL:0000084!1.31e-08!25;CL:0000827!1.31e-08!25;CL:0000945!3.34e-07!24;CL:0000826!3.34e-07!24;CL:0000134!6.26e-07!358
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002390!1.12e-31!102;UBERON:0003061!1.12e-31!102;UBERON:0002193!6.69e-27!112;UBERON:0002371!7.16e-24!80;UBERON:0001474!7.83e-23!86;UBERON:0002405!1.20e-17!115;UBERON:0004765!1.30e-15!101;UBERON:0001434!1.30e-15!101
}}

Latest revision as of 11:35, 17 September 2013


Full id: C999_CD14_Eosinophils_Mast_Neutrophils_CD19_CD8_CD4



Phase1 CAGE Peaks

Hg19::chr11:65337828..65337854,-p1@LOC254100
Hg19::chr11:82868189..82868212,+p1@PCF11
Hg19::chr13:52027161..52027179,-p1@INTS6
Hg19::chr16:89557354..89557392,+p@chr16:89557354..89557392
+
Hg19::chr18:60193965..60193978,-p@chr18:60193965..60193978
-
Hg19::chr19:47729523..47729537,+p@chr19:47729523..47729537
+
Hg19::chr20:49126881..49126936,+p1@PTPN1
Hg19::chr2:118771594..118771685,-p1@CCDC93


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:0005849mRNA cleavage factor complex0.00988864149387627
GO:0044451nucleoplasm part0.00988864149387627
GO:0005654nucleoplasm0.00988864149387627
GO:0006379mRNA cleavage0.00988864149387627
GO:0006396RNA processing0.00988864149387627
GO:0016073snRNA metabolic process0.00988864149387627
GO:0016180snRNA processing0.00988864149387627
GO:0032039integrator complex0.00988864149387627
GO:0031981nuclear lumen0.00988864149387627
GO:0044446intracellular organelle part0.0119162554456562
GO:0044422organelle part0.0119162554456562
GO:0031974membrane-enclosed lumen0.0134872640129136
GO:0043233organelle lumen0.0134872640129136
GO:0008286insulin receptor signaling pathway0.0147213814335944
GO:0044428nuclear part0.015180302815631
GO:0016591DNA-directed RNA polymerase II, holoenzyme0.0461787976172104



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
leukocyte1.85e-53136
hematopoietic stem cell5.64e-53168
angioblastic mesenchymal cell5.64e-53168
hematopoietic cell3.47e-50177
hematopoietic oligopotent progenitor cell3.02e-49161
hematopoietic multipotent progenitor cell3.02e-49161
hematopoietic lineage restricted progenitor cell3.82e-44120
nongranular leukocyte6.43e-42115
myeloid leukocyte1.29e-3172
myeloid cell1.69e-31108
common myeloid progenitor1.69e-31108
granulocyte monocyte progenitor cell4.26e-2867
myeloid lineage restricted progenitor cell4.28e-2766
classical monocyte7.36e-2642
CD14-positive, CD16-negative classical monocyte7.36e-2642
macrophage dendritic cell progenitor2.55e-2561
defensive cell3.54e-2548
phagocyte3.54e-2548
monopoietic cell2.29e-2459
monocyte2.29e-2459
monoblast2.29e-2459
promonocyte2.29e-2459
nucleate cell5.06e-1655
lymphocyte1.62e-1553
common lymphoid progenitor1.62e-1553
lymphoid lineage restricted progenitor cell2.25e-1552
mature alpha-beta T cell3.74e-0918
alpha-beta T cell3.74e-0918
immature T cell3.74e-0918
mature T cell3.74e-0918
immature alpha-beta T cell3.74e-0918
T cell3.76e-0825
pro-T cell3.76e-0825
lymphocyte of B lineage5.43e-0724
pro-B cell5.43e-0724
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.17e-3198
blood island5.17e-3198
hemolymphoid system9.49e-27108
bone marrow5.33e-2376
bone element8.36e-2282
immune system6.64e-2193
skeletal element1.75e-1690
skeletal system1.09e-13100
blood5.24e-0715
haemolymphatic fluid5.24e-0715
organism substance5.24e-0715


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)
MA0003.13.24424
MA0004.11.15451
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.11.78293
MA0017.10.337901
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.653157
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.283474
MA0056.10
MA0057.10.632427
MA0058.12.55421
MA0059.11.69011
MA0060.11.67203
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.823119
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.215282
MA0074.11.36092
MA0076.10.985027
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.441522
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.13.13688
MA0095.10
MA0098.10
MA0100.11.40058
MA0101.10.825856
MA0103.10.291333
MA0105.10.586268
MA0106.11.45807
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.10.231781
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.11.60834
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.470675
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.480646
MA0146.11.63914
MA0147.11.26392
MA0148.10.480298
MA0149.10.506665
MA0062.21.50503
MA0035.20.515566
MA0039.24.9691
MA0138.22.6595
MA0002.20.179788
MA0137.20.321796
MA0104.21.66814
MA0047.20.586412
MA0112.20.208783
MA0065.20.226158
MA0150.11.00335
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.274121
MA0155.11.64163
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.243637
MA0160.10.495355
MA0161.10
MA0162.12.66274
MA0163.10.493198
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.26.37808
MA0102.21.46209
MA0258.10.603127
MA0259.10.699589
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
ATF3#46738.423690447253280.004171166389609930.0198728363927043
BRCA1#672410.09211532161190.000358706566497560.00358703131926836
CCNT2#90564.752151182721970.0003235895417103970.00331164803005312
CHD2#110645.172011417058430.004437884607941780.0210065369184568
E2F1#186974.293965563019419.58670853279727e-050.00137097939539479
E2F4#187457.917537697052780.0001399334011451070.00182590011021912
E2F6#187653.135722332310870.01024880501420960.0381554538508907
EGR1#195853.117611934256340.01051390990388360.0389273339638293
ELF1#199784.258097958807549.24826870984006e-060.000246775660650737
ELK4#200536.088380621925510.01034377041843630.0384172488880181
ETS1#211344.864380461101170.0055537915159820.0251379228628605
FOS#235355.6237220680590.000709701815129380.00570377436477855
FOXA1#316945.540709874692730.003444272925946160.017524915722152
GABPB1#255365.300762877136630.000173452943092670.00211158082802837
GTF2F1#296257.962288047973530.0001362053831339150.00178126145869308
HEY1#2346284.040111043105711.4081650274634e-050.000339569030947242
HMGN3#932455.111592327094120.001109515975889930.0077096965406499
IRF1#365965.727872815172930.0001111980671919970.0015449534308188
IRF3#3661211.74548805287240.01164488049453140.0425356629115965
MAX#414964.839416631755340.0002917504313705360.00309813149993975
MXI1#460144.980785814379650.005094415320429170.0236995831470068
MYC#460963.916711403707050.0009649270569246440.00694049703155323
NFKB1#479074.802055496169614.48248622098168e-050.00079414143924191
NFYA#480049.212790349915260.0005085231351680210.00445625505234208
NFYB#480136.284922470076170.009473769012482620.0357001970735945
PBX3#5090616.43588451505812.33030791475828e-071.227926479866e-05
POLR2A#543082.147453176558070.002210725788971910.0127315131334126
POU2F2#545266.829593043306894.02833503357943e-050.000738615313504217
RDBP#7936238.40960099750620.001154787820652850.00789712448933755
REST#597856.031267947580010.0005105473532543910.00443013085963238
RFX5#599346.023955413597550.00252649680619860.0139929363070783
SIN3A#2594285.408884726815141.36410592556506e-065.35988934387092e-05
SP1#666764.273786033605670.0005904726864288940.00494494241824611
SP2#666839.807573935191740.002707184665085610.0148902285252199
SREBF1#6720317.62719354018310.0004972605150068210.00439591932679849
SRF#672246.89858913108390.001522071904568780.00970237229255732
TAF1#687272.925165500027130.001265325357915740.00849397834267657
TAF7#687945.716534702461960.003068541555180160.0161782730820062
TAL1#6886311.20073125404010.00185069994516520.0109324237315106
TBP#690862.780078015322290.006390181121263010.0278065133170946
TFAP2A#702036.194487889891860.009861483862380290.0370529397432413
TFAP2C#702245.404614304930110.003775146896547010.0186505471489344
USF1#739164.771124457905970.0003163361106003810.00324090906955005
YY1#752874.297274406122129.53674534900876e-050.00136514274603224
ZBTB33#10009311.87427188624290.001564551645953250.00992590264559054



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:C999&oldid=3068116"