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Coexpression cluster:C297: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.420729,0.489223,2.25148,0.207099,0.524307,1.19919,0.607241,0.525756,0.514838,2.18293,0.175016,0.106075,0.509367,0.582785,0.790489,0.0696425,1.1296,0.202022,0.139008,0.441244,0.018269,0.516133,0.436898,0.147292,0.278454,0.117348,0.410879,0.432758,0.31569,0.128939,0.637759,0.232273,0.0652651,0.121537,0.239312,0.0612706,0.23327,0.790097,0.0876637,0.162148,0.112484,0.93224,0.248733,1.10539,0.837852,0.770074,0.609574,0.374854,0.209884,0.0587231,0.393538,1.56826,0.595464,0.78018,0.403288,0.588993,0.0127239,1.34079,0.219543,0.241801,0.260471,1.03043,0.0420792,0.190343,0.317164,0.169322,0.476019,0.804487,0.639886,0.65579,1.27209,1.36087,0.0617527,1.03733,0.0518917,0.282296,0.0743914,0.531474,0.223148,0.110846,0.147561,0.189673,0.0955211,1.33646,0.360923,0.0108577,0.583446,0.00883533,0.138597,0.897729,0.555976,0.340047,0.2437,0.294093,0.310659,0.180922,0.0254419,0.273528,0.857645,0.387068,0.0889071,0.239834,0.269554,0.60454,0.488909,1.06146,3.2345,1.45055,0.115485,0.728703,0.0898848,0.737994,1.32475,0.41221,0.514502,0.405198,0.0205902,0.989723,0.502242,0.164063,0.395035,0.841064,0.446509,0.100785,0.61111,0.180363,0.283346,0.690819,0.429542,0.528384,0.340576,0.360222,3.97807,0.670261,0.567222,2.58267,1.86108,1.16169,0.530357,1.33715,0.947435,0.498402,0.0840508,1.36805,1.51823,0.233537,0.467489,1.1816,0.13698,1.26789,2.19865,0.724345,0.903383,0.181426,0.0873671,0.683452,1.90379,2.24309,0.278548,1.90005,0.497369,0.871921,0.222625,0.451948,0.514937,0.0951573,0.631628,0.604395,0.00431188
|tfbs_overrepresentation_jaspar=MA0003.1;0.144741,MA0004.1;0.404373,MA0006.1;0.305199,MA0007.1;0.161987,MA0009.1;0.309236,MA0014.1;0.546942,MA0017.1;0.203459,MA0019.1;1.17544,MA0024.1;0.660306,MA0025.1;1.8723,MA0027.1;1.81465,MA0028.1;3.02225,MA0029.1;0.24734,MA0030.1;0.672868,MA0031.1;1.08481,MA0038.1;0.0872867,MA0040.1;0.251423,MA0041.1;0.0539262,MA0042.1;0.379428,MA0043.1;0.833138,MA0046.1;0.301098,MA0048.1;0.319872,MA0050.1;0.16788,MA0051.1;0.0854137,MA0052.1;0.254136,MA0055.1;0.0217289,MA0056.1;0,MA0057.1;0.423246,MA0058.1;0.455338,MA0059.1;0.452115,MA0060.1;0.51646,MA0061.1;1.06881,MA0063.1;0,MA0066.1;3.40919,MA0067.1;1.39883,MA0068.1;0.0828759,MA0069.1;0.807779,MA0070.1;0.289965,MA0071.1;0.070878,MA0072.1;0.781548,MA0073.1;1.44858e-05,MA0074.1;0.288254,MA0076.1;2.56299,MA0077.1;0.281032,MA0078.1;0.829152,MA0081.1;0.73346,MA0083.1;0.314889,MA0084.1;0.739331,MA0087.1;0.284873,MA0088.1;0.0310472,MA0089.1;0,MA0090.1;0.12095,MA0091.1;0.182723,MA0092.1;0.340194,MA0093.1;0.31174,MA0095.1;0,MA0098.1;0,MA0100.1;0.0935814,MA0101.1;0.318901,MA0103.1;0.48921,MA0105.1;0.653621,MA0106.1;0.106627,MA0107.1;0.175927,MA0108.2;0.194591,MA0109.1;0,MA0111.1;0.899363,MA0113.1;0.114834,MA0114.1;0.167469,MA0115.1;0.50405,MA0116.1;0.329589,MA0117.1;1.60866,MA0119.1;0.0189922,MA0122.1;0.357986,MA0124.1;0.468805,MA0125.1;0.399431,MA0130.1;0,MA0131.1;2.02373,MA0132.1;0,MA0133.1;0,MA0135.1;0.332279,MA0136.1;1.05099,MA0139.1;0.969765,MA0140.1;0.245432,MA0141.1;0.447779,MA0142.1;0.176637,MA0143.1;0.114924,MA0144.1;0.0033417,MA0145.1;0.0798025,MA0146.1;0.749888,MA0147.1;0.0859124,MA0148.1;1.68086,MA0149.1;0.0660182,MA0062.2;5.67889,MA0035.2;0.0695343,MA0039.2;0.0915651,MA0138.2;0.420466,MA0002.2;4.54474,MA0137.2;0.592243,MA0104.2;0.196978,MA0047.2;1.12265,MA0112.2;0.269149,MA0065.2;0.219643,MA0150.1;0.826572,MA0151.1;0,MA0152.1;0.072456,MA0153.1;1.00274,MA0154.1;1.02982,MA0155.1;0.0998378,MA0156.1;2.58933,MA0157.1;0.483135,MA0158.1;0,MA0159.1;0.0288354,MA0160.1;0.221938,MA0161.1;0,MA0162.1;0.0557542,MA0163.1;0.034371,MA0164.1;0.770869,MA0080.2;1.92343,MA0018.2;5.34018,MA0099.2;0.253365,MA0079.2;0.0392803,MA0102.2;0.773745,MA0258.1;0.408158,MA0259.1;0.832475,MA0442.1;0
}}
}}

Revision as of 19:01, 22 January 2013


Full id: C297_Eosinophils_CD4_Basophils_Natural_Neutrophils_CD8_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:35416142..35416169,+p3@CREM
Hg19::chr10:35416172..35416184,+p13@CREM
Hg19::chr11:3862855..3862867,+p@chr11:3862855..3862867
+
Hg19::chr12:106697097..106697117,-p@chr12:106697097..106697117
-
Hg19::chr14:52314051..52314062,-p@chr14:52314051..52314062
-
Hg19::chr17:38497640..38497647,+p27@RARA
Hg19::chr17:62097904..62097915,-p4@ICAM2
Hg19::chr17:76837188..76837205,+p@chr17:76837188..76837205
+
Hg19::chr19:41769066..41769091,+p@chr19:41769066..41769091
+
Hg19::chr19:59085102..59085126,+p@chr19:59085102..59085126
+
Hg19::chr1:185536411..185536432,+p@chr1:185536411..185536432
+
Hg19::chr1:198650975..198650986,-p@chr1:198650975..198650986
-
Hg19::chr1:198651031..198651051,-p@chr1:198651031..198651051
-
Hg19::chr1:198651180..198651193,+p@chr1:198651180..198651193
+
Hg19::chr1:198651195..198651213,+p@chr1:198651195..198651213
+
Hg19::chr1:45273151..45273188,+p@chr1:45273151..45273188
+
Hg19::chr20:34356239..34356262,+p@chr20:34356239..34356262
+
Hg19::chr20:42839727..42839752,+p1@LOC100505783
Hg19::chr20:43150543..43150551,-p@chr20:43150543..43150551
-
Hg19::chr20:43150846..43150896,+p@chr20:43150846..43150896
+
Hg19::chr20:43150918..43150934,+p@chr20:43150918..43150934
+
Hg19::chr20:5590658..5590681,+p@chr20:5590658..5590681
+
Hg19::chr22:39097139..39097148,+p@chr22:39097139..39097148
+
Hg19::chr22:47158371..47158384,-p@chr22:47158371..47158384
-
Hg19::chr2:170441202..170441230,-p@chr2:170441202..170441230
-
Hg19::chr2:197034975..197035000,-p@chr2:197034975..197035000
-
Hg19::chr2:197035024..197035040,-p@chr2:197035024..197035040
-
Hg19::chr2:55845186..55845202,+p@chr2:55845186..55845202
+
Hg19::chr2:97204412..97204438,-p@chr2:97204412..97204438
-
Hg19::chr4:152020461..152020473,-p@chr4:152020461..152020473
-
Hg19::chr6:108145154..108145165,-p@chr6:108145154..108145165
-
Hg19::chr7:36816762..36816783,-p@chr7:36816762..36816783
-
Hg19::chr7:66146955..66146980,-p@chr7:66146955..66146980
-
Hg19::chr7:66309834..66309894,-p1@LOC729156
Hg19::chr7:75796016..75796041,+p@chr7:75796016..75796041
+
Hg19::chr8:118532766..118532792,-p@chr8:118532766..118532792
-
Hg19::chr8:64080945..64080978,-p@chr8:64080945..64080978
-
Hg19::chr9:100684655..100684671,+p@chr9:100684655..100684671
+
Hg19::chr9:132650707..132650725,-p8@FNBP1
Hg19::chr9:132650755..132650788,-p4@FNBP1
Hg19::chr9:132650792..132650809,-p12@FNBP1
Hg19::chr9:33159824..33159848,+p@chr9:33159824..33159848
+


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
6.41827216562196e-050.040627662808387273Notch up reg. targets (Netpath):NetPath_3



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:0003713transcription coactivator activity0.0112437650335631
GO:0008140cAMP response element binding protein binding0.0112437650335631
GO:0003712transcription cofactor activity0.0112437650335631
GO:0016563transcription activator activity0.0112437650335631
GO:0008134transcription factor binding0.0175123136485932
GO:0003708retinoic acid receptor activity0.0378801066558398



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
leukocyte2.77e-92136
hematopoietic stem cell5.88e-76168
angioblastic mesenchymal cell5.88e-76168
nongranular leukocyte7.76e-72115
hematopoietic lineage restricted progenitor cell1.36e-71120
hematopoietic cell1.32e-70177
hematopoietic oligopotent progenitor cell1.85e-67161
hematopoietic multipotent progenitor cell1.85e-67161
classical monocyte5.30e-5142
CD14-positive, CD16-negative classical monocyte5.30e-5142
myeloid leukocyte7.92e-4772
defensive cell6.82e-4348
phagocyte6.82e-4348
granulocyte monocyte progenitor cell6.76e-3767
macrophage dendritic cell progenitor1.69e-3561
myeloid lineage restricted progenitor cell5.02e-3466
monopoietic cell2.36e-3359
monocyte2.36e-3359
monoblast2.36e-3359
promonocyte2.36e-3359
myeloid cell3.20e-33108
common myeloid progenitor3.20e-33108
lymphoid lineage restricted progenitor cell1.24e-3252
lymphocyte8.83e-3253
common lymphoid progenitor8.83e-3253
nucleate cell3.58e-3055
mature alpha-beta T cell3.14e-2318
alpha-beta T cell3.14e-2318
immature T cell3.14e-2318
mature T cell3.14e-2318
immature alpha-beta T cell3.14e-2318
mesenchymal cell6.09e-21354
connective tissue cell5.34e-20361
T cell8.52e-1925
pro-T cell8.52e-1925
stuff accumulating cell7.50e-1887
motile cell1.05e-16386
CD8-positive, alpha-beta T cell2.32e-1511
intermediate monocyte2.95e-149
CD14-positive, CD16-positive monocyte2.95e-149
granulocyte3.23e-148
multi fate stem cell9.53e-13427
stem cell1.07e-12441
somatic stem cell3.29e-12433
CD4-positive, alpha-beta T cell2.83e-116
lymphocyte of B lineage2.91e-1124
pro-B cell2.91e-1124
B cell6.37e-1114
blood cell8.86e-1011
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.01e-3898
blood island1.01e-3898
hemolymphoid system1.03e-34108
bone marrow1.65e-3276
immune system9.55e-3293
bone element4.67e-2982
skeletal element3.46e-2590
skeletal system3.01e-21100
connective tissue1.02e-18371
lateral plate mesoderm1.37e-10203
musculoskeletal system1.21e-07167


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)
MA0003.10.144741
MA0004.10.404373
MA0006.10.305199
MA0007.10.161987
MA0009.10.309236
MA0014.10.546942
MA0017.10.203459
MA0019.11.17544
MA0024.10.660306
MA0025.11.8723
MA0027.11.81465
MA0028.13.02225
MA0029.10.24734
MA0030.10.672868
MA0031.11.08481
MA0038.10.0872867
MA0040.10.251423
MA0041.10.0539262
MA0042.10.379428
MA0043.10.833138
MA0046.10.301098
MA0048.10.319872
MA0050.10.16788
MA0051.10.0854137
MA0052.10.254136
MA0055.10.0217289
MA0056.10
MA0057.10.423246
MA0058.10.455338
MA0059.10.452115
MA0060.10.51646
MA0061.11.06881
MA0063.10
MA0066.13.40919
MA0067.11.39883
MA0068.10.0828759
MA0069.10.807779
MA0070.10.289965
MA0071.10.070878
MA0072.10.781548
MA0073.11.44858e-05
MA0074.10.288254
MA0076.12.56299
MA0077.10.281032
MA0078.10.829152
MA0081.10.73346
MA0083.10.314889
MA0084.10.739331
MA0087.10.284873
MA0088.10.0310472
MA0089.10
MA0090.10.12095
MA0091.10.182723
MA0092.10.340194
MA0093.10.31174
MA0095.10
MA0098.10
MA0100.10.0935814
MA0101.10.318901
MA0103.10.48921
MA0105.10.653621
MA0106.10.106627
MA0107.10.175927
MA0108.20.194591
MA0109.10
MA0111.10.899363
MA0113.10.114834
MA0114.10.167469
MA0115.10.50405
MA0116.10.329589
MA0117.11.60866
MA0119.10.0189922
MA0122.10.357986
MA0124.10.468805
MA0125.10.399431
MA0130.10
MA0131.12.02373
MA0132.10
MA0133.10
MA0135.10.332279
MA0136.11.05099
MA0139.10.969765
MA0140.10.245432
MA0141.10.447779
MA0142.10.176637
MA0143.10.114924
MA0144.10.0033417
MA0145.10.0798025
MA0146.10.749888
MA0147.10.0859124
MA0148.11.68086
MA0149.10.0660182
MA0062.25.67889
MA0035.20.0695343
MA0039.20.0915651
MA0138.20.420466
MA0002.24.54474
MA0137.20.592243
MA0104.20.196978
MA0047.21.12265
MA0112.20.269149
MA0065.20.219643
MA0150.10.826572
MA0151.10
MA0152.10.072456
MA0153.11.00274
MA0154.11.02982
MA0155.10.0998378
MA0156.12.58933
MA0157.10.483135
MA0158.10
MA0159.10.0288354
MA0160.10.221938
MA0161.10
MA0162.10.0557542
MA0163.10.034371
MA0164.10.770869
MA0080.21.92343
MA0018.25.34018
MA0099.20.253365
MA0079.20.0392803
MA0102.20.773745
MA0258.10.408158
MA0259.10.832475
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#46784.278699909715950.0004663231207055730.00429170958788943
BATF#10538105.799476617215155.93965793861152e-060.00017815391598238
BCL11A#53335117.430095384278041.60966870389735e-078.91368980733483e-06
BCL3#60254.112750333778370.007083034499878040.0295389945347108
BCLAF1#9774147.217549203373953.07699218625634e-092.57292223331005e-07
BRCA1#672178.169807641304864.96860992546389e-126.49457637053221e-10
BRF2#552904102.3405315614627.88423726816163e-084.71874989140133e-06
CCNT2#905172.564653019246780.0001085459125704390.00151071782555226
CEBPB#1051203.79578458372612.93067916697899e-081.99269011406327e-06
CHD2#1106133.201721353417120.0001096654379979560.0015250797175857
CTCF#10664172.169627579577990.000844294016354890.00636658648188364
CTCFL#140690104.701541514041513.63874760731806e-050.000704145194294406
E2F4#187492.714584353275240.004824661988887480.0226382816720918
E2F6#1876192.269665688148820.0001824568162161910.00221011452433342
EBF1#1879173.604998485516031.11799004160593e-064.60417042410418e-05
EGR1#1958252.969154223101272.39834497378206e-081.68673906206616e-06
ELF1#1997272.737348687804852.16864782773001e-081.53657673324488e-06
ELK4#2005124.638766188133725.72957160997209e-060.000172397213878961
EP300#2033182.903117882667091.07598646932828e-050.000279053764266642
ETS1#2113153.474557472215129.80106808828958e-060.000257189384440421
FOS#2353132.785081405133980.0004405220379280360.00410416423899787
FOSL2#2355135.240300187126245.30749507015305e-072.47459588228444e-05
FOXA1#3169133.429963255762165.39654083920658e-050.000914950208938143
GABPB1#2553213.533841918091093.76526773060242e-082.4951827190126e-06
GATA1#262392.905780316528670.003069829661269730.0161826135671992
GTF2B#295986.084539035109384.18112365998534e-050.000757585659134645
GTF2F1#2962144.246553625585882.13268969595545e-067.75813232866217e-05
HEY1#23462282.693407362070471.22115425605082e-089.09024442962877e-07
HMGN3#9324163.115637227943081.76253764855585e-050.000402443527497866
IRF1#3659152.727558483415680.0001686044960766620.00206120624672252
IRF4#3662136.78306345065892.69676201628614e-081.85538292634327e-06
JUND#3727182.997713117944736.81826711745991e-060.000198188978424825
MAX#4149203.072645480479589.91561689780469e-074.20282919314052e-05
MEF2A#4205125.355208831326871.29637386153801e-065.15190219654369e-05
MEF2C#420898.85243310556236.12772843712137e-072.81183580951019e-05
MXI1#4601194.506425260629214.80064081371731e-093.87161487215306e-07
MYC#4609253.108501114053229.1160011331437e-096.96463820295826e-07
NFKB1#4790283.658708949462566.95021977783518e-128.85212199240645e-10
NFYB#480183.192341572102180.003041821609101670.0160471186054943
NRF1#489992.616488453080910.006131293458304640.0271091891745429
PAX5#5079264.12877866215775.12966171779913e-126.68000922874343e-10
PBX3#509094.695967004302319.65983251816607e-050.00137503509385954
POLR2A#5430402.045193501483881.34958418921476e-111.66213706529953e-09
POU2F2#5452214.553062028871263.75602121697042e-103.73595333218261e-08
RAD21#5885122.958581112987520.0004535969171531480.0042173247067175
REST#5978112.527388473271620.002986984463435450.0158797490647358
RFX5#5993236.597665452987791.26053327826328e-142.1688440699924e-12
RXRA#625694.301703672671410.0001872675035127390.0022647094487456
SIN3A#25942303.863489090582241.04916321365618e-131.64032270765026e-11
SIX5#14791272.84778589257650.01038085244441590.0385440076949073
SMC3#9126113.940339554625276.90500969681743e-050.00110099588965789
SP1#6667283.79892091876062.70412291122094e-123.63469617406698e-10
SP2#666874.35892174897410.0009897172147747680.00710412894803175
SPI1#6688224.297502790178573.34981793693828e-103.3639580338067e-08
SRF#6722206.570084886746581.69092484396929e-122.32366447078038e-10
STAT1#677273.451097916199870.003716320439153190.0187411294227291
STAT3#6774133.256024880071559.23444819976633e-050.00134378784385592
TAF1#6872342.706275564650951.14184188233196e-111.42306472970009e-09
TAF7#6879112.994375320337220.0007547943065901110.00593554420495178
TBP#6908343.000719127649464.66216504574772e-136.82905827788002e-11
TCF12#6938215.317232451093212.04337792876457e-112.45296951152003e-09
TCF7L2#6934123.077193303753530.000316052753437910.00323832370414029
USF1#7391142.120499759069320.003707991434821470.0187018359714743
USF2#7392103.093380329778470.001079963216966110.00762354027825098
YY1#7528222.572518011828214.28712985869587e-060.000135638762590833
ZEB1#693583.216844193817880.002901896662633210.0156820441658258
ZNF263#10127122.349097610574480.003410825010177240.0173826747298053



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

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