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{{Coexpression_clusters
{
|full_id=C265_CD4_Eosinophils_CD14_Natural_CD19_Basophils_CD8
|

Latest revision as of 11:09, 17 September 2013


Full id: C265_CD4_Eosinophils_CD14_Natural_CD19_Basophils_CD8



Phase1 CAGE Peaks

Hg19::chr10:1094998..1095041,+p1@uc001igd.2
Hg19::chr10:27443390..27443429,+p2@MASTL
Hg19::chr10:35416125..35416138,+p10@CREM
Hg19::chr10:52384324..52384340,-p@chr10:52384324..52384340
-
Hg19::chr11:102217835..102217893,-p@chr11:102217835..102217893
-
Hg19::chr11:506455..506475,+p1@AK095144
Hg19::chr11:58345569..58345646,-p2@LPXN
Hg19::chr11:6633553..6633568,+p@chr11:6633553..6633568
+
Hg19::chr12:12714174..12714202,+p@chr12:12714174..12714202
+
Hg19::chr12:22697211..22697230,+p@chr12:22697211..22697230
+
Hg19::chr12:25539120..25539152,-p@chr12:25539120..25539152
-
Hg19::chr12:92270935..92270983,-p@chr12:92270935..92270983
-
Hg19::chr13:22178048..22178078,+p@chr13:22178048..22178078
+
Hg19::chr13:50699797..50699825,+p1@FLJ31945
Hg19::chr13:52377944..52378010,+p1@ENST00000456688
Hg19::chr13:52378231..52378277,-p2@DHRS12
Hg19::chr13:52378340..52378382,+p2@ENST00000456688
Hg19::chr14:64970670..64970712,-p3@ZBTB25
Hg19::chr14:78227105..78227137,+p2@C14orf178
Hg19::chr14:81685812..81685827,+p@chr14:81685812..81685827
+
Hg19::chr15:31620147..31620158,-p@chr15:31620147..31620158
-
Hg19::chr15:31620170..31620188,-p@chr15:31620170..31620188
-
Hg19::chr15:45492834..45492856,+p@chr15:45492834..45492856
+
Hg19::chr15:72766533..72766572,-p@chr15:72766533..72766572
-
Hg19::chr18:11908408..11908445,+p@chr18:11908408..11908445
+
Hg19::chr1:174968752..174968799,-p1@BC038430
Hg19::chr1:179851611..179851688,-p1@BC069736
Hg19::chr1:62901922..62901944,-p@chr1:62901922..62901944
-
Hg19::chr22:42228870..42228891,-p@chr22:42228870..42228891
-
Hg19::chr22:42228898..42228928,-p@chr22:42228898..42228928
-
Hg19::chr2:157198383..157198413,+p@chr2:157198383..157198413
+
Hg19::chr2:235355325..235355351,+p@chr2:235355325..235355351
+
Hg19::chr2:235355717..235355722,+p@chr2:235355717..235355722
+
Hg19::chr2:61698499..61698527,+p@chr2:61698499..61698527
+
Hg19::chr2:85555169..85555184,+p@chr2:85555169..85555184
+
Hg19::chr3:142297846..142297858,+p@chr3:142297846..142297858
+
Hg19::chr4:4250016..4250052,+p@chr4:4250016..4250052
+
Hg19::chr5:98265404..98265448,-p@chr5:98265404..98265448
-
Hg19::chr6:158245076..158245129,-p@chr6:158245076..158245129
-
Hg19::chr7:139875446..139875459,+p@chr7:139875446..139875459
+
Hg19::chr7:158622384..158622412,+p@chr7:158622384..158622412
+
Hg19::chr7:158622429..158622444,+p@chr7:158622429..158622444
+
Hg19::chr7:17980172..17980237,+p1@AK096065
Hg19::chr7:44646370..44646405,-p@chr7:44646370..44646405
-
Hg19::chr8:123794727..123794742,-p@chr8:123794727..123794742
-
Hg19::chr9:132175926..132175968,-p@chr9:132175926..132175968
-
Hg19::chr9:6757547..6757566,-p@chr9:6757547..6757566
-
Hg19::chr9:6757859..6757874,-p@chr9:6757859..6757874
-
Hg19::chrX:123094129..123094146,-p@chrX:123094129..123094146
-


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:0032311angiogenin-PRI complex0.0259579720862203
GO:0008428ribonuclease inhibitor activity0.0259579720862203
GO:0008140cAMP response element binding protein binding0.0259579720862203



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
leukocyte2.15e-55136
hematopoietic lineage restricted progenitor cell3.97e-46120
nongranular leukocyte1.46e-44115
hematopoietic stem cell2.63e-44168
angioblastic mesenchymal cell2.63e-44168
hematopoietic cell1.79e-43177
hematopoietic oligopotent progenitor cell3.19e-40161
hematopoietic multipotent progenitor cell3.19e-40161
classical monocyte6.68e-2742
CD14-positive, CD16-negative classical monocyte6.68e-2742
myeloid leukocyte2.74e-2672
defensive cell6.13e-2448
phagocyte6.13e-2448
granulocyte monocyte progenitor cell8.14e-2467
myeloid lineage restricted progenitor cell9.30e-2366
macrophage dendritic cell progenitor9.38e-2261
nucleate cell9.82e-2255
lymphocyte2.72e-2153
common lymphoid progenitor2.72e-2153
lymphoid lineage restricted progenitor cell4.56e-2152
monopoietic cell1.29e-2059
monocyte1.29e-2059
monoblast1.29e-2059
promonocyte1.29e-2059
myeloid cell8.33e-19108
common myeloid progenitor8.33e-19108
mature alpha-beta T cell3.63e-1218
alpha-beta T cell3.63e-1218
immature T cell3.63e-1218
mature T cell3.63e-1218
immature alpha-beta T cell3.63e-1218
T cell2.08e-1125
pro-T cell2.08e-1125
stuff accumulating cell1.77e-0987
lymphocyte of B lineage6.58e-0924
pro-B cell6.58e-0924
B cell4.59e-0814
CD8-positive, alpha-beta T cell1.34e-0711
intermediate monocyte2.42e-079
CD14-positive, CD16-positive monocyte2.42e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.16e-2898
blood island1.16e-2898
hemolymphoid system1.53e-26108
bone marrow1.22e-2076
immune system1.36e-2093
bone element4.74e-1882
skeletal element3.84e-1490
skeletal system8.63e-12100
adult organism5.59e-08114
lateral plate mesoderm3.01e-07203
blood3.68e-0715
haemolymphatic fluid3.68e-0715
organism substance3.68e-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)
MA0003.18.4605
MA0004.10.564226
MA0006.12.3476
MA0007.10.278299
MA0009.10.729191
MA0014.18.90237
MA0017.10.139299
MA0019.10.27961
MA0024.10.193834
MA0025.10.952648
MA0027.11.74826
MA0028.14.06487
MA0029.10.206098
MA0030.10.198787
MA0031.10.15963
MA0038.10.495033
MA0040.10.603427
MA0041.10.339523
MA0042.10.119762
MA0043.11.34208
MA0046.10.256123
MA0048.10.52932
MA0050.10.531914
MA0051.11.27109
MA0052.10.609377
MA0055.10.065659
MA0056.10
MA0057.11.50382
MA0058.11.1913
MA0059.10.56087
MA0060.11.53658
MA0061.10.998985
MA0063.10
MA0066.10.229222
MA0067.11.27961
MA0068.10.698909
MA0069.10.253439
MA0070.10.245703
MA0071.10.0505283
MA0072.10.24262
MA0073.10.208921
MA0074.10.223426
MA0076.12.63472
MA0077.10.237364
MA0078.10.340465
MA0081.10.334083
MA0083.11.36088
MA0084.10.679402
MA0087.10.240948
MA0088.10.760901
MA0089.10
MA0090.10.0824972
MA0091.10.132783
MA0092.10.0240824
MA0093.10.871434
MA0095.10
MA0098.10
MA0100.10.522734
MA0101.10.615386
MA0103.10.0898466
MA0105.13.08807
MA0106.10.977503
MA0107.10.545054
MA0108.20.477395
MA0109.10
MA0111.10.0915545
MA0113.10.0873401
MA0114.10.202063
MA0115.10.449785
MA0116.10.220033
MA0117.10.290704
MA0119.10.300181
MA0122.10.309767
MA0124.10.415762
MA0125.10.349207
MA0130.10
MA0131.11.76232
MA0132.10
MA0133.10
MA0135.10.285448
MA0136.10.236422
MA0139.11.72414
MA0140.10.415677
MA0141.10.165669
MA0142.10.141688
MA0143.10.294674
MA0144.10.173752
MA0145.10.573811
MA0146.12.08174
MA0147.10.575059
MA0148.10.350475
MA0149.10.0465992
MA0062.25.18556
MA0035.20.0494386
MA0039.23.06895
MA0138.20.697089
MA0002.20.187747
MA0137.20.0429195
MA0104.20.715585
MA0047.20.553745
MA0112.21.91516
MA0065.20.16838
MA0150.10.201453
MA0151.10
MA0152.10.0518114
MA0153.10.336269
MA0154.10.275458
MA0155.11.31596
MA0156.10.123394
MA0157.10.126996
MA0158.10
MA0159.10.228971
MA0160.10.0431262
MA0161.10
MA0162.12.50994
MA0163.13.11212
MA0164.10.0928538
MA0080.20.383846
MA0018.23.29424
MA0099.20.192957
MA0079.25.82629
MA0102.20.713248
MA0258.10.0769964
MA0259.11.838
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#467125.501185598206221.18585786823215e-064.82845262769193e-05
BCLAF1#977493.977016907981560.0003643466253222930.0036368151774859
BHLHE40#855376.410259078139630.0001027616377835390.00143710801934589
BRCA1#672114.531153817866562.21715017652059e-050.000485444333932146
CCNT2#905314.008617324200858.06396210264447e-141.2760486939971e-11
CEBPB#1051172.765500196714735.58404995787418e-050.000943066936530435
CHD2#1106173.588742615918091.73006809458607e-066.52298128990884e-05
CTBP2#148845.119755129741070.007730253402104120.0318163521206838
CTCF#10664222.406645718523482.31179848306162e-050.000504686291330418
CTCFL#14069072.820924908424910.01128838175918480.0414188906178857
E2F1#1869404.006032012146396.40540940858776e-201.61198687523734e-17
E2F4#1874194.912105020212332.03255772399953e-091.75147109023751e-07
E2F6#1876383.890855465397976.46745685155434e-181.41902253386446e-15
EBF1#1879132.362940183783610.002362508301357790.013389299136396
EGR1#1958303.053987200904173.6253968623884e-103.62675117730826e-08
ELF1#1997342.954598583662371.31063476127527e-111.62181734399085e-09
ELK4#2005144.638766188133729.66692069300339e-074.1074187561293e-05
EP300#2033162.211899339174920.001292432116283410.00866202385885408
ETS1#2113173.37528440158044.01365311537851e-060.00012965725880514
FOSL2#2355144.837200172731915.86191261122966e-072.69697044583355e-05
FOXA1#3169184.070725622223231.14729927301646e-076.65312541779932e-06
FOXA2#3170115.529287781210573.41569904988976e-060.000113935545535432
GABPB1#2553223.173245804000162.05522055036064e-071.1035741853939e-05
GATA1#2623133.597632772845023.96023418025606e-050.000738444737639283
GTF2B#295974.563404276332030.0007956398411549630.00614614122562006
GTF2F1#2962174.419882344997559.05083970660663e-085.34649687849711e-06
HDAC2#3066102.737881680944130.002921782723990410.0157854257881555
HEY1#23462423.462952322662044.1603653191097e-199.89759438638948e-17
HMGN3#9324254.172728430280914.78373384157692e-115.40701708528628e-09
HSF1#3297310.0586122448980.003363998340704770.0173489024099978
IRF1#3659243.740651634398651.42394454138473e-091.274338851394e-07
IRF4#366273.130644669534880.006552629287133130.0280092518364055
JUN#3725143.575094054953241.97220037995901e-050.000441437281359921
JUNB#372695.622361100783472.64819100181548e-050.00057037413907735
JUND#3727263.711454336502992.10546935672642e-102.17071188694127e-08
MAX#4149263.423804963962961.26089494517609e-091.14510093199344e-07
MEF2A#4205103.825149165233480.0002242269747414780.00248493644047381
MEF2C#420875.901622070374860.0001708064118275540.00208349110544942
MXI1#4601153.049460702681425.93528028297096e-050.00098034910244062
MYC#4609343.623624155810612.79903604832913e-144.65491283202939e-12
NANOG#7992363.58099328338930.006328612505674530.0275581204753228
NFKB1#4790333.696042714252995.87975187250173e-149.49111910065236e-12
NFYA#480093.384290332621930.001156364207900260.00790686928826079
NFYB#480182.736292776087580.008033446840236980.032209964471265
NR3C1#2908103.055719047178170.00129579623688420.0086834560913666
NRF1#4899153.737840647258445.27766341971107e-060.0001614037744923
PAX5#5079233.130612392185511.1632558148794e-076.7419130993446e-06
PBX3#509083.577879622325570.001580934995527690.00996386880682615
POLR2A#5430482.103627601526273.09308838190185e-155.56005262508515e-13
POU2F2#5452305.575177994536243.65022295288725e-177.5341034580354e-15
REST#5978203.938787231072662.84928677417381e-081.94113934382217e-06
RFX5#5993204.917514623344946.2442975793816e-105.97205306678604e-08
SETDB1#986975.760003739715780.0001980787664131720.00237947415291296
SIN3A#25942343.753103687994189.5353800974906e-151.65426173090004e-12
SMARCB1#6598145.215061651759262.36554145992893e-071.24273030449456e-05
SMC3#9126103.070394458149560.001249739927546650.00840177587982265
SP1#6667242.791043940313914.64982889759276e-072.2003782520874e-05
SPI1#6688172.846397951936463.85539760633801e-050.000724718989575837
SREBF1#672054.796515249029420.003811381661291130.0188242168411796
SREBF2#6721326.75162831089880.0002027855095931740.00240831428660467
SRF#6722123.378900798898240.0001525884296881570.00194580989111128
STAT1#677272.958083928171310.008831209132892060.0335329085849887
TAF1#6872443.001919113730472.90003442941987e-186.51347732847703e-16
TAF7#6879225.13321483486382.45701050058341e-112.90938457676226e-09
TBP#6908413.101583636141871.81894286409033e-163.60471677007077e-14
TCF7L2#6934163.516792347146895.07044190547414e-060.000156440733283845
TFAP2A#7020113.708264859254990.0001353300496605910.00177292210944587
TFAP2C#7022153.308947533630682.28581321579838e-050.00049911780565496
THAP1#5514563.841119747287920.004524196548603040.0213879487298367
TRIM28#10155124.552781643737768.28679503509411e-060.000229080091760242
USF1#7391222.856183348950511.30558131929861e-065.18454781012274e-05
USF2#7392174.507497051962926.80931366643833e-084.13945232834199e-06
WRNIP1#5689748.964895048928660.001047707838144140.00740585847092626
YY1#7528333.307523158064841.53068063760009e-122.11179333038726e-10
ZBTB33#1000963.877313268977280.004323673954582750.0205254629155758
ZBTB7A#51341233.450896205737671.84164723609789e-081.32283215743348e-06
ZEB1#6935103.446618779090580.0005132235236031470.00444780944167198
ZNF143#770292.479752836123490.009132338096998520.0345469522787753
ZNF263#10127152.516890297044080.0005043696059751260.00444372003361196



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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