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Coexpression cluster:C399: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=1.33106,0.842854,0.499626,0.138052,0.182732,0.137092,0.184184,0.610783,0.183905,2.11345,0.765118,0.213274,0.442432,1.00561,0.0480727,0.45628,0.916161,0.0308524,1.05652,0.840448,0.0649159,0.903095,2.59478,0.0467386,0.289071,1.211,0.585217,0.815439,0.415824,0.512987,0.711692,0.376235,1.9312,0.259921,1.37136,0.0584656,1.81976,0.843204,0.288032,2.39911,0.144755,0.672435,0.407233,0.179554,0.737913,0.962947,1.0385,0.738491,0.072488,0.416095,1.24926,1.06944,0.535117,0.439939,0.572791,0.528367,0.0513042,0.477592,0.079352,0.925954,1.05528,1.6501,0.184676,0.867421,0.575973,0.298136,0.652492,0.998973,0.963046,0.844111,2.16207,0.0766341,3.29527,0.571009,2.5331,0.602561,0.340028,0.83793,0.365188,0.589587,0.0108677,0.865542,0.198116,0.0744849,1.30381,4.06757,0.412821,1.00333,1.31981,1.09502,0.738491,2.16741,0.389962,0.0241172,2.08608,0.114934,0.280717,0.425289,1.33236,0.887162,0.290547,0.385331,0.420622,0.349541,0.289379,0.753978,1.60555,0.518366,2.69242,1.04013,0.524704,1.07356,0.487406,0.788408,0.694065,0.141384,2.95962,1.16849,0.803521,0.0248267,0.563638,0.256203,0.135489,0.205724,0.797035,0.839253,0.531855,1.0207,0.601752,0.278686,0.502548,0.354419,0.61471,0.203467,0.750477,0.284207,0.697219,0.411536,0.711091,1.54156,1.14596,0.676716,0.181176,0.422337,0.790737,0.906885,0.278155,1.3843,0.323374,0.466161,2.24453,5.7196,0.50288,0.340314,0.186129,0.873115,0.246224,0.677151,0.289148,0.537765,0.675601,0.486836,0.364552,0.545057,0.30298,0.197587,1.42543,0.183316,2.74946
|tfbs_overrepresentation_for_novel_motifs=1.33106,0.842854,0.499626,0.138052,0.182732,0.137092,0.184184,0.610783,0.183905,2.11345,0.765118,0.213274,0.442432,1.00561,0.0480727,0.45628,0.916161,0.0308524,1.05652,0.840448,0.0649159,0.903095,2.59478,0.0467386,0.289071,1.211,0.585217,0.815439,0.415824,0.512987,0.711692,0.376235,1.9312,0.259921,1.37136,0.0584656,1.81976,0.843204,0.288032,2.39911,0.144755,0.672435,0.407233,0.179554,0.737913,0.962947,1.0385,0.738491,0.072488,0.416095,1.24926,1.06944,0.535117,0.439939,0.572791,0.528367,0.0513042,0.477592,0.079352,0.925954,1.05528,1.6501,0.184676,0.867421,0.575973,0.298136,0.652492,0.998973,0.963046,0.844111,2.16207,0.0766341,3.29527,0.571009,2.5331,0.602561,0.340028,0.83793,0.365188,0.589587,0.0108677,0.865542,0.198116,0.0744849,1.30381,4.06757,0.412821,1.00333,1.31981,1.09502,0.738491,2.16741,0.389962,0.0241172,2.08608,0.114934,0.280717,0.425289,1.33236,0.887162,0.290547,0.385331,0.420622,0.349541,0.289379,0.753978,1.60555,0.518366,2.69242,1.04013,0.524704,1.07356,0.487406,0.788408,0.694065,0.141384,2.95962,1.16849,0.803521,0.0248267,0.563638,0.256203,0.135489,0.205724,0.797035,0.839253,0.531855,1.0207,0.601752,0.278686,0.502548,0.354419,0.61471,0.203467,0.750477,0.284207,0.697219,0.411536,0.711091,1.54156,1.14596,0.676716,0.181176,0.422337,0.790737,0.906885,0.278155,1.3843,0.323374,0.466161,2.24453,5.7196,0.50288,0.340314,0.186129,0.873115,0.246224,0.677151,0.289148,0.537765,0.675601,0.486836,0.364552,0.545057,0.30298,0.197587,1.42543,0.183316,2.74946
|tfbs_overrepresentation_jaspar=MA0003.1;4.73368,MA0004.1;1.26901,MA0006.1;1.55549,MA0007.1;0.731569,MA0009.1;0.46676,MA0014.1;8.37467,MA0017.1;0.226532,MA0019.1;0.21677,MA0024.1;0.986236,MA0025.1;0.584598,MA0027.1;2.02165,MA0028.1;0.439907,MA0029.1;0.394311,MA0030.1;0.384823,MA0031.1;0.33249,MA0038.1;0.186009,MA0040.1;0.399176,MA0041.1;0.133492,MA0042.1;0.115387,MA0043.1;1.17884,MA0046.1;0.457379,MA0048.1;1.71454,MA0050.1;0.115873,MA0051.1;1.03176,MA0052.1;0.402401,MA0055.1;4.6364,MA0056.1;0,MA0057.1;1.00962,MA0058.1;1.92954,MA0059.1;0.54521,MA0060.1;0.901878,MA0061.1;0.291177,MA0063.1;0,MA0066.1;1.04408,MA0067.1;0.753856,MA0068.1;1.48376,MA0069.1;1.15094,MA0070.1;0.44448,MA0071.1;0.160989,MA0072.1;0.44064,MA0073.1;3.35339,MA0074.1;0.538325,MA0076.1;0.585118,MA0077.1;0.434073,MA0078.1;0.252504,MA0081.1;0.256536,MA0083.1;0.473254,MA0084.1;0.931415,MA0087.1;0.438554,MA0088.1;2.26293,MA0089.1;0,MA0090.1;0.088522,MA0091.1;0.124326,MA0092.1;0.103692,MA0093.1;1.57294,MA0095.1;0,MA0098.1;0,MA0100.1;0.195288,MA0101.1;0.736489,MA0103.1;0.0445972,MA0105.1;0.900038,MA0106.1;1.15327,MA0107.1;0.271434,MA0108.2;0.879282,MA0109.1;0,MA0111.1;0.316029,MA0113.1;0.225587,MA0114.1;0.490033,MA0115.1;0.682809,MA0116.1;0.82319,MA0117.1;1.24828,MA0119.1;0.0665855,MA0122.1;0.522217,MA0124.1;0.644657,MA0125.1;1.39486,MA0130.1;0,MA0131.1;0.734231,MA0132.1;0,MA0133.1;0,MA0135.1;0.493123,MA0136.1;0.557618,MA0139.1;0.697372,MA0140.1;0.15932,MA0141.1;0.0728657,MA0142.1;0.307468,MA0143.1;0.225712,MA0144.1;0.0218306,MA0145.1;0.885121,MA0146.1;7.25248,MA0147.1;1.64637,MA0148.1;0.425644,MA0149.1;0.153304,MA0062.2;1.03976,MA0035.2;0.158878,MA0039.2;5.92019,MA0138.2;1.30278,MA0002.2;0.330883,MA0137.2;0.0564642,MA0104.2;1.65224,MA0047.2;0.59341,MA0112.2;0.430193,MA0065.2;0.109893,MA0150.1;0.0856547,MA0151.1;0,MA0152.1;0.163454,MA0153.1;0.553438,MA0154.1;0.163462,MA0155.1;0.76997,MA0156.1;0.458984,MA0157.1;0.286356,MA0158.1;0,MA0159.1;0.840798,MA0160.1;0.448616,MA0161.1;0,MA0162.1;6.94987,MA0163.1;2.75536,MA0164.1;0.661297,MA0080.2;1.11612,MA0018.2;0.615632,MA0099.2;0.16368,MA0079.2;13.2029,MA0102.2;0.967149,MA0258.1;0.0873009,MA0259.1;1.2606,MA0442.1;0
}}
}}

Revision as of 19:08, 22 January 2013


Full id: C399_CD19_Eosinophils_CD4_CD8_CD14_Basophils_Natural



Phase1 CAGE Peaks

Hg19::chr10:32635996..32636023,-p4@EPC1
Hg19::chr10:32636038..32636099,-p1@EPC1
Hg19::chr12:92539614..92539630,-p1@BTG1
Hg19::chr15:72766701..72766713,+p2@ARIH1
Hg19::chr15:93426049..93426068,+p1@LOC100507217
Hg19::chr16:11836574..11836590,-p2@TXNDC11
Hg19::chr18:9102437..9102446,-p@chr18:9102437..9102446
-
Hg19::chr18:9136862..9136875,+p3@ANKRD12
Hg19::chr19:18112033..18112073,+p3@ARRDC2
Hg19::chr19:39898362..39898396,+p@chr19:39898362..39898396
+
Hg19::chr19:41869996..41870017,-p2@B9D2
Hg19::chr19:41870026..41870062,-p1@B9D2
Hg19::chr1:204380872..204380883,-p5@PPP1R15B
Hg19::chr22:29664309..29664322,+p2@EWSR1
Hg19::chr2:197036244..197036255,-p3@STK17B
Hg19::chr2:241499761..241499793,+p1@DUSP28
Hg19::chr2:24583284..24583310,-p3@ITSN2
Hg19::chr2:30369859..30369880,+p1@YPEL5
Hg19::chr3:156877896..156877946,-p1@CCNL1
Hg19::chr4:77997196..77997224,+p@chr4:77997196..77997224
+
Hg19::chr5:179125566..179125638,-p@chr5:179125566..179125638
-
Hg19::chr6:151712673..151712709,-p1@ZBTB2
Hg19::chr7:130792754..130792811,-p1@ENST00000423414
Hg19::chr7:32931356..32931379,-p1@KBTBD2
Hg19::chr9:100684772..100684816,-p1@C9orf156
Hg19::chr9:86322808..86322826,-p3@UBQLN1


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
leukocyte2.60e-52136
hematopoietic stem cell8.57e-44168
angioblastic mesenchymal cell8.57e-44168
hematopoietic lineage restricted progenitor cell5.68e-42120
nongranular leukocyte8.01e-41115
hematopoietic oligopotent progenitor cell9.19e-40161
hematopoietic multipotent progenitor cell9.19e-40161
hematopoietic cell2.32e-39177
myeloid leukocyte1.63e-2672
classical monocyte8.03e-2442
CD14-positive, CD16-negative classical monocyte8.03e-2442
granulocyte monocyte progenitor cell4.17e-2367
myeloid lineage restricted progenitor cell3.24e-2166
defensive cell3.99e-2148
phagocyte3.99e-2148
macrophage dendritic cell progenitor8.88e-2161
myeloid cell2.52e-20108
common myeloid progenitor2.52e-20108
monopoietic cell1.00e-1959
monocyte1.00e-1959
monoblast1.00e-1959
promonocyte1.00e-1959
lymphoid lineage restricted progenitor cell8.55e-1952
lymphocyte1.21e-1853
common lymphoid progenitor1.21e-1853
nucleate cell2.80e-1855
mature alpha-beta T cell2.14e-1018
alpha-beta T cell2.14e-1018
immature T cell2.14e-1018
mature T cell2.14e-1018
immature alpha-beta T cell2.14e-1018
T cell4.74e-1025
pro-T cell4.74e-1025
lymphocyte of B lineage3.05e-0824
pro-B cell3.05e-0824
B cell2.48e-0714
mesenchymal cell7.85e-07354
CD8-positive, alpha-beta T cell9.08e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.34e-2798
blood island5.34e-2798
hemolymphoid system1.09e-23108
bone marrow2.84e-1976
immune system3.80e-1893
bone element5.27e-1882
skeletal element2.03e-1390
adult organism2.95e-11114
skeletal system1.26e-10100
blood6.83e-0715
haemolymphatic fluid6.83e-0715
organism substance6.83e-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)
MA0003.14.73368
MA0004.11.26901
MA0006.11.55549
MA0007.10.731569
MA0009.10.46676
MA0014.18.37467
MA0017.10.226532
MA0019.10.21677
MA0024.10.986236
MA0025.10.584598
MA0027.12.02165
MA0028.10.439907
MA0029.10.394311
MA0030.10.384823
MA0031.10.33249
MA0038.10.186009
MA0040.10.399176
MA0041.10.133492
MA0042.10.115387
MA0043.11.17884
MA0046.10.457379
MA0048.11.71454
MA0050.10.115873
MA0051.11.03176
MA0052.10.402401
MA0055.14.6364
MA0056.10
MA0057.11.00962
MA0058.11.92954
MA0059.10.54521
MA0060.10.901878
MA0061.10.291177
MA0063.10
MA0066.11.04408
MA0067.10.753856
MA0068.11.48376
MA0069.11.15094
MA0070.10.44448
MA0071.10.160989
MA0072.10.44064
MA0073.13.35339
MA0074.10.538325
MA0076.10.585118
MA0077.10.434073
MA0078.10.252504
MA0081.10.256536
MA0083.10.473254
MA0084.10.931415
MA0087.10.438554
MA0088.12.26293
MA0089.10
MA0090.10.088522
MA0091.10.124326
MA0092.10.103692
MA0093.11.57294
MA0095.10
MA0098.10
MA0100.10.195288
MA0101.10.736489
MA0103.10.0445972
MA0105.10.900038
MA0106.11.15327
MA0107.10.271434
MA0108.20.879282
MA0109.10
MA0111.10.316029
MA0113.10.225587
MA0114.10.490033
MA0115.10.682809
MA0116.10.82319
MA0117.11.24828
MA0119.10.0665855
MA0122.10.522217
MA0124.10.644657
MA0125.11.39486
MA0130.10
MA0131.10.734231
MA0132.10
MA0133.10
MA0135.10.493123
MA0136.10.557618
MA0139.10.697372
MA0140.10.15932
MA0141.10.0728657
MA0142.10.307468
MA0143.10.225712
MA0144.10.0218306
MA0145.10.885121
MA0146.17.25248
MA0147.11.64637
MA0148.10.425644
MA0149.10.153304
MA0062.21.03976
MA0035.20.158878
MA0039.25.92019
MA0138.21.30278
MA0002.20.330883
MA0137.20.0564642
MA0104.21.65224
MA0047.20.59341
MA0112.20.430193
MA0065.20.109893
MA0150.10.0856547
MA0151.10
MA0152.10.163454
MA0153.10.553438
MA0154.10.163462
MA0155.10.76997
MA0156.10.458984
MA0157.10.286356
MA0158.10
MA0159.10.840798
MA0160.10.448616
MA0161.10
MA0162.16.94987
MA0163.12.75536
MA0164.10.661297
MA0080.21.11612
MA0018.20.615632
MA0099.20.16368
MA0079.213.2029
MA0102.20.967149
MA0258.10.0873009
MA0259.11.2606
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#46765.183809506002020.0008273772749530850.00629630247878354
BCL11A#5333544.364531554401090.01239829597958810.0448858026141222
BCLAF1#977475.829558971955880.0001350674306231760.00177036990296861
BHLHE40#855346.903355930304220.00248780081019080.0139705037539261
BRCA1#67296.986849068808232.58784030664677e-069.09086625583188e-05
CCNT2#905245.848801455657821.32418394561589e-172.82814820237583e-15
CEBPB#1051103.065826009932620.0007515812418635480.00591651415685438
CHD2#1106124.774164384977011.74393283855153e-066.56814286785008e-05
E2F1#1869203.77491478067649.60121071657053e-108.94505661041846e-08
E2F4#1874115.359563979543421.86077042754615e-066.8694592676738e-05
E2F6#1876183.473415506559737.23098834621988e-084.38049415249917e-06
EGR1#1958193.645207800053568.2202698188689e-096.33591704511327e-07
ELF1#1997203.275459968313491.31285266114889e-089.67628927859767e-07
EP300#203392.344825982154180.009553706652143490.0359780611200813
ESR1#209944.733631276331460.00940422384463920.0354829383710359
ETS1#2113165.986929798278362.97244571629203e-103.01105003068694e-08
FOS#235382.768601633505970.005730189157185770.0258266539524997
FOSL2#235563.906969370283470.003497469076466230.0177618367555097
FOXA1#316983.409667615195520.001547942133790880.00983785848664185
GABPB1#2553123.262007924391778.86511950721784e-050.00129854728781813
GATA1#262363.129301879338560.01022312492299060.0380707057882766
GTF2B#295956.143044218139280.001138870934123560.00779746568040712
GTF2F1#296294.409882611185340.0001024233803515150.00143276124036055
HEY1#23462253.884722156832411.36461192838341e-142.33254836642283e-12
HMGN3#9324154.718392917317654.1343190520398e-082.7241902048958e-06
IRF1#3659144.112318944226728.83175437084568e-073.8146385224845e-05
JUND#3727102.690255362258090.002091474499676320.0121142202468912
MAFF#2376436.497925748839830.01072147509855170.0395765785818979
MAX#4149133.226277754503564.1487443708495e-050.000752240821783249
MEF2A#420553.604467482623860.01108747707795980.0407805958283163
MXI1#4601134.980785814379653.06881462572476e-071.54236732770004e-05
MYC#4609234.61971088642374.34307927397279e-147.09838585750304e-12
NFE2#477838.908183921341820.004516815805865380.0213540231745405
NFKB1#4790214.432666611848877.47810368726604e-129.47822416255313e-10
NFYA#480074.960733265338990.0003640375606225740.00363407749893529
NFYB#4801106.446074328283251.24498959010537e-065.01448005403066e-05
NR3C1#290884.60708410189940.0002068702496962860.00243166257828142
NRF1#4899115.165887458646922.67099421510522e-069.35152413112215e-05
PAX5#5079194.87391327278384.91758369800027e-115.55229755497784e-09
PBX3#509097.585792853103741.31297329626767e-065.20598398211464e-05
POLR2A#5430262.147453176558072.33941527921015e-091.99612902242997e-07
POU2F2#5452175.954004191600885.7086217815449e-116.38332709039366e-09
RDBP#7936317.72750815269520.0006394588000991690.00524251806449149
REST#5978145.196169308684324.69219230234018e-083.0513566118562e-06
RFX5#5993125.56057422793623.3852741247177e-071.68119184170895e-05
SIN3A#25942214.368714587042999.99266059084579e-121.24984847838005e-09
SIX5#14791274.600269518777420.0005738431549014780.00484491554201742
SMARCB1#659853.510137650222580.01234152275505920.0447143653304526
SP1#6667173.725864747245978.7004172652649e-085.15992548987508e-06
SP2#666866.035430113964150.000370620861049520.00368675798715599
SPI1#668882.524407233391610.009961584420652570.0373685541219257
SRF#672273.714624916737490.002015141964666310.0117143165784139
TAF1#6872263.343046285745292.34697364575191e-143.93443949580551e-12
TAF7#6879135.716534702461966.06106722496615e-083.76344708625588e-06
TBP#6908233.27906637704688.65288496924105e-119.45291478349965e-09
TCF12#6938104.090178808533246.9255380418476e-050.00109940153146758
TCF7L2#6934104.142375601206676.2149001869846e-050.00101800182030816
TFAP2A#702074.447324638896720.0007023535805431760.00564732509033403
TFAP2C#702283.325916495341610.001817120947696520.0109024125154522
THAP1#5514544.826022246592510.008800237171279350.0334250270913643
TRIM28#1015553.575100970242790.01146093152189210.0419268004909066
USF1#7391174.159441835097511.60784907091647e-081.17100522397103e-06
USF2#7392104.996998994257541.21892050374788e-050.000303390940159496
YY1#7528213.966714836420426.80357818903111e-117.51119347234905e-09
ZBTB33#1000944.871496158458640.0085206820409780.0324777923969964
ZBTB7A#51341102.827657426106110.001422792114418130.00917083167547459
ZNF143#770284.154115862223970.0004190616856614870.0039206649994446
ZNF263#1012782.529797426772520.009837217318819780.0369724031797977



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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