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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,0

Latest revision as of 11:14, 17 September 2013


Full id: C290_Eosinophils_CD14_Basophils_Mast_CD4_CD8_immature



Phase1 CAGE Peaks

Hg19::chr10:104155305..104155351,-p@chr10:104155305..104155351
-
Hg19::chr10:27444072..27444081,-p9@YME1L1
Hg19::chr10:27444113..27444140,-p3@YME1L1
Hg19::chr11:35068956..35068967,-p@chr11:35068956..35068967
-
Hg19::chr11:35068999..35069019,-p@chr11:35068999..35069019
-
Hg19::chr11:35104126..35104150,-p@chr11:35104126..35104150
-
Hg19::chr12:31945225..31945237,-p1@H3F3C
Hg19::chr12:62996849..62996863,+p@chr12:62996849..62996863
+
Hg19::chr14:103243813..103243954,+p1@TRAF3
Hg19::chr14:24711615..24711644,+p@chr14:24711615..24711644
+
Hg19::chr14:24711941..24711990,+p@chr14:24711941..24711990
+
Hg19::chr14:35344580..35344591,-p3@BAZ1A
Hg19::chr15:45003493..45003500,-p5@PATL2
Hg19::chr15:66084428..66084478,-p1@DENND4A
Hg19::chr17:39845134..39845142,+p1@EIF1
Hg19::chr17:56415424..56415454,-p@chr17:56415424..56415454
-
Hg19::chr17:63053123..63053164,+p@chr17:63053123..63053164
+
Hg19::chr17:73775848..73775868,-p1@H3F3A
p1@H3F3B
Hg19::chr18:11851403..11851428,+p1@CHMP1B
Hg19::chr18:48405312..48405340,-p@chr18:48405312..48405340
-
Hg19::chr19:47616682..47616696,+p@chr19:47616682..47616696
+
Hg19::chr19:48825442..48825465,+p@chr19:48825442..48825465
+
Hg19::chr1:181057828..181057846,+p1@IER5
Hg19::chr1:203274370..203274382,-p3@ENST00000432511
Hg19::chr1:204380531..204380560,+p1@BC009873
Hg19::chr1:45275366..45275381,-p@chr1:45275366..45275381
-
Hg19::chr1:46153015..46153034,+p2@TMEM69
Hg19::chr1:66801861..66801890,-p@chr1:66801861..66801890
-
Hg19::chr20:44600810..44600853,-p1@ZNF335
Hg19::chr2:128145779..128145837,+p@chr2:128145779..128145837
+
Hg19::chr3:195269598..195269612,+p@chr3:195269598..195269612
+
Hg19::chr4:80993447..80993469,+p@chr4:80993447..80993469
+
Hg19::chr5:40680009..40680062,+p1@PTGER4
Hg19::chr6:138188378..138188415,+p1@TNFAIP3
Hg19::chr6:143267648..143267661,-p@chr6:143267648..143267661
-
Hg19::chr6:16760246..16760257,+p@chr6:16760246..16760257
+
Hg19::chr6:31240053..31240069,+p@chr6:31240053..31240069
+
Hg19::chr6:43192145..43192186,-p@chr6:43192145..43192186
-
Hg19::chr7:115851107..115851141,-p2@uc003vhn.1
Hg19::chr8:101962922..101962946,+p@chr8:101962922..101962946
+
Hg19::chr8:123793988..123794016,+p1@ZHX2
Hg19::chr9:3526360..3526421,-p5@RFX3
Hg19::chr9:91925676..91925735,-p@chr9:91925676..91925735
-
Hg19::chr9:96329032..96329074,+p@chr9:96329032..96329074
+


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:0050789regulation of biological process0.0148046825618672
GO:0065007biological regulation0.0157128152988876
GO:0050794regulation of cellular process0.0247774628528408
GO:0000228nuclear chromosome0.0273609379661523
GO:0044424intracellular part0.0273609379661523
GO:0003677DNA binding0.0273609379661523
GO:0001740Barr body0.0273609379661523
GO:0000805X chromosome0.0273609379661523
GO:0043231intracellular membrane-bound organelle0.0273609379661523
GO:0043227membrane-bound organelle0.0273609379661523
GO:0010468regulation of gene expression0.0292000980264414
GO:0000803sex chromosome0.0292000980264414
GO:0001739sex chromatin0.0292000980264414
GO:0031323regulation of cellular metabolic process0.0292000980264414
GO:0043124negative regulation of I-kappaB kinase/NF-kappaB cascade0.0313510836916462
GO:0019222regulation of metabolic process0.0322328454910958
GO:0008270zinc ion binding0.0322328454910958
GO:0005634nucleus0.0388675441935308
GO:0043283biopolymer metabolic process0.0388675441935308
GO:0005720nuclear heterochromatin0.0452201402484462
GO:0003676nucleic acid binding0.0452201402484462
GO:0016481negative regulation of transcription0.0452201402484462
GO:0043229intracellular organelle0.0452201402484462
GO:0043226organelle0.0452201402484462
GO:0006355regulation of transcription, DNA-dependent0.0452201402484462
GO:0046914transition metal ion binding0.0452201402484462
GO:0044464cell part0.0452201402484462
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0452201402484462
GO:0004957prostaglandin E receptor activity0.0452201402484462
GO:0006351transcription, DNA-dependent0.0452201402484462
GO:0032774RNA biosynthetic process0.0452201402484462
GO:0030278regulation of ossification0.0455985375246441
GO:0005622intracellular0.0455985375246441
GO:0000792heterochromatin0.0459337836461696
GO:0048523negative regulation of cellular process0.0459337836461696
GO:0004955prostaglandin receptor activity0.0459337836461696
GO:0000790nuclear chromatin0.0459337836461696
GO:0045449regulation of transcription0.0459337836461696
GO:0031324negative regulation of cellular metabolic process0.0459337836461696
GO:0046850regulation of bone remodeling0.0459337836461696
GO:0048519negative regulation of biological process0.0459337836461696
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0459337836461696
GO:0004953icosanoid receptor activity0.0459337836461696
GO:0003705RNA polymerase II transcription factor activity, enhancer binding0.0459337836461696
GO:0004954prostanoid receptor activity0.0459337836461696
GO:0006350transcription0.0459337836461696
GO:0010467gene expression0.0459337836461696
GO:0006402mRNA catabolic process0.0471613307300842
GO:0009892negative regulation of metabolic process0.0488373563300737



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
leukocyte8.31e-87136
hematopoietic stem cell4.66e-72168
angioblastic mesenchymal cell4.66e-72168
hematopoietic cell2.22e-69177
hematopoietic lineage restricted progenitor cell2.71e-68120
nongranular leukocyte3.18e-67115
hematopoietic oligopotent progenitor cell6.85e-66161
hematopoietic multipotent progenitor cell6.85e-66161
classical monocyte3.23e-4342
CD14-positive, CD16-negative classical monocyte3.23e-4342
myeloid leukocyte4.76e-4172
defensive cell4.78e-3648
phagocyte4.78e-3648
granulocyte monocyte progenitor cell7.42e-3667
lymphocyte1.48e-3253
common lymphoid progenitor1.48e-3253
lymphoid lineage restricted progenitor cell3.55e-3252
myeloid lineage restricted progenitor cell6.64e-3266
macrophage dendritic cell progenitor1.84e-3161
myeloid cell2.16e-31108
common myeloid progenitor2.16e-31108
nucleate cell7.25e-3155
monopoietic cell9.19e-3059
monocyte9.19e-3059
monoblast9.19e-3059
promonocyte9.19e-3059
mesenchymal cell7.69e-19354
connective tissue cell6.80e-18361
T cell2.25e-1625
pro-T cell2.25e-1625
mature alpha-beta T cell4.03e-1618
alpha-beta T cell4.03e-1618
immature T cell4.03e-1618
mature T cell4.03e-1618
immature alpha-beta T cell4.03e-1618
lymphocyte of B lineage7.21e-1424
pro-B cell7.21e-1424
motile cell1.85e-13386
stuff accumulating cell1.16e-1287
multi fate stem cell9.00e-12427
stem cell1.68e-11441
somatic stem cell3.23e-11433
B cell5.56e-1014
CD8-positive, alpha-beta T cell7.24e-1011
intermediate monocyte1.52e-099
CD14-positive, CD16-positive monocyte1.52e-099
granulocyte2.72e-098
blood cell7.89e-0811
CD4-positive, alpha-beta T cell1.83e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.85e-4698
blood island4.85e-4698
hemolymphoid system5.44e-43108
immune system1.14e-3393
bone marrow2.49e-3276
bone element8.93e-2982
skeletal element8.52e-2590
skeletal system1.51e-21100
connective tissue1.31e-16371
lateral plate mesoderm2.10e-13203
blood4.19e-1015
haemolymphatic fluid4.19e-1015
organism substance4.19e-1015
musculoskeletal system1.05e-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)
MA0003.13.43597
MA0004.10.667193
MA0006.10.472818
MA0007.10.0371799
MA0009.10.295212
MA0014.14.136
MA0017.10.0700225
MA0019.10.100079
MA0024.10.631021
MA0025.10.398381
MA0027.11.79461
MA0028.11.90879
MA0029.10.234549
MA0030.10.2268
MA0031.10.185022
MA0038.10.273665
MA0040.10.238542
MA0041.10.0483802
MA0042.10.0386689
MA0043.10.801467
MA0046.10.28722
MA0048.10.104718
MA0050.10.986706
MA0051.10.567488
MA0052.10.241195
MA0055.10.452808
MA0056.10
MA0057.11.89213
MA0058.11.82335
MA0059.10.215837
MA0060.12.22852
MA0061.17.21125
MA0063.10
MA0066.10.274169
MA0067.11.36262
MA0068.10.131442
MA0069.10.284408
MA0070.10.276295
MA0071.10.229527
MA0072.10.273057
MA0073.10.5611
MA0074.10.565906
MA0076.11.48375
MA0077.10.267535
MA0078.10.124992
MA0081.11.00438
MA0083.11.47643
MA0084.10.721137
MA0087.10.271301
MA0088.10.39874
MA0089.10
MA0090.10.492569
MA0091.10.166703
MA0092.10.132641
MA0093.11.40426
MA0095.10
MA0098.10
MA0100.10.0858032
MA0101.15.02474
MA0103.10.0439436
MA0105.15.90075
MA0106.10.0982452
MA0107.16.77418
MA0108.20.539294
MA0109.10
MA0111.10.285301
MA0113.10.702295
MA0114.10.0641411
MA0115.10.487485
MA0116.10.0709472
MA0117.10.32334
MA0119.10.19322
MA0122.10.343167
MA0124.10.452592
MA0125.10.384032
MA0130.10
MA0131.11.94371
MA0132.10
MA0133.10
MA0135.10.317863
MA0136.10.591381
MA0139.11.13421
MA0140.10.0632888
MA0141.10.0842661
MA0142.10.165691
MA0143.10.34524
MA0144.10.125436
MA0145.10.633287
MA0146.12.34032
MA0147.10.998465
MA0148.10.188509
MA0149.10.471821
MA0062.22.97812
MA0035.20.0630244
MA0039.25.85295
MA0138.20.125638
MA0002.20.262615
MA0137.20.012513
MA0104.21.49598
MA0047.20.0926231
MA0112.20.434463
MA0065.20.114546
MA0150.10.254396
MA0151.10
MA0152.10.0657794
MA0153.10.370648
MA0154.10.406183
MA0155.10.518687
MA0156.11.16677
MA0157.10.149753
MA0158.10
MA0159.10.165973
MA0160.10.0556436
MA0161.10
MA0162.15.56609
MA0163.11.33387
MA0164.10.3612
MA0080.21.40484
MA0018.22.22995
MA0099.20.0659162
MA0079.26.58763
MA0102.20.755388
MA0258.10.112476
MA0259.10.519751
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#46773.573686856410480.003106546740880540.0163332981811731
BCL3#602129.421937128292273.0434066534761e-092.54687778431403e-07
BCLAF1#9774104.921056275027692.56364832317549e-050.000554566833521385
BRCA1#67273.211127602331050.005572312444001770.0252151966784706
CCNT2#905223.168100788481321.33016809544966e-077.57891029572651e-06
CHD2#1106122.821097136577320.0007277179508223390.00580390493057918
CTCF#10664151.827360127184670.01097590308418210.040380172685955
E2F1#1869273.011352472766863.72381991061812e-093.05748449406483e-07
E2F4#1874144.030746463954144.26193893615668e-060.000135005350486281
E2F6#1876242.736630399107663.95038382298945e-071.91538596141687e-05
EBF1#1879153.03629551587585.30616995055974e-050.000900066726435779
EGR1#1958313.514398907707147.2196106577002e-131.03857977614263e-10
ELF1#1997333.193573469105657.6460260582827e-131.09539549451439e-10
ELK4#200593.320934884686640.001255172464212140.00843558281787977
EP300#2033162.463251536808440.0003339185903812990.00340003155511675
ETS1#2113132.874406636105240.0003405576949417810.00346122081568944
FOS#2353132.658486795809710.000724364347524680.0057789235422145
FOSL2#2355103.847772864673110.0001991431690888240.00239116043187718
GABPB1#2553182.891325205710891.28776074496936e-050.000315709963483227
GATA1#2623134.006454678850131.11010742851811e-050.000284441878623657
GTF2B#2959107.259961348710058.38897660627985e-073.65056803243026e-05
GTF2F1#2962133.763990713587492.16259023031474e-050.000476193887969304
HEY1#23462322.938262576804153.08465847714837e-113.55976405187733e-09
HMGN3#9324244.46102603091851.80238990752895e-112.17870138370851e-09
IRF1#3659203.471438069801771.59551320186378e-078.84937882578073e-06
IRF3#366144.271086564680870.01414884872864330.0496436072153052
IRF4#366283.98445685213530.0007604344365475460.00597225237769507
JUN#372592.559442334796070.007197860559491440.029819014635967
JUND#3727182.861453430765421.48954987896922e-050.000353080117588892
MAX#4149172.493032810298210.0001700213557209510.00207682577428542
MEF2A#420572.98187764471610.008260715353555660.0325501169896246
MEF2C#420887.511155362295289.53985594576662e-060.000253390899064069
MXI1#4601112.490392907189820.003452243906819740.0175483744468192
MYC#4609232.729829160159468.93997301163262e-073.85182277789563e-05
NANOG#7992363.987924338319910.003690962125865960.0186231408987543
NFKB1#4790293.617132711400484.52174270108211e-125.94020485482156e-10
NFYA#480093.768868779510790.0005095799980131140.0044643927030024
NFYB#4801114.189948313384114.13201003684635e-050.000750248602639423
NR2C2#718253.706205784686460.01088197403469390.0401264868202307
NRF1#4899123.330076213012060.0001582765238295020.00199496039973803
PAX5#5079294.395850009185392.75268485180949e-144.58513003569588e-12
POLR2A#5430412.001035914520025.27129681590154e-115.91966632425743e-09
POU2F2#5452275.587848853614731.2692889424603e-152.36298160181125e-13
RDBP#7936517.4589095443211.01923052103961e-050.000266384925893032
REST#5978132.851144847946920.0003687532919612770.00367132746035689
RFX5#5993154.107242327452871.35237203105121e-065.31978841999839e-05
RXRA#625683.649930388933320.001338262532308110.00887239259897963
SIN3A#25942273.319088355091113.92732006451198e-103.8804671732977e-08
SMARCB1#6598114.563178945289351.8836493517578e-050.000427480344737576
SMC3#912682.735442335442340.007798008499468870.0320333625580565
SP1#6667243.108208024440493.22972172072396e-082.17338213138331e-06
SPI1#6688173.169852264656517.43411407159201e-060.000212948831465441
SREBF1#672044.273259040044390.01412491015224240.0495646101330526
STAT3#6774102.390787499353240.007255711670666720.0300277092713886
TAF1#6872382.887176337689121.07374624158114e-141.85356997891723e-12
TAF7#6879164.15747978360874.44122303686873e-072.11507931029427e-05
TBP#6908363.032812380351595.06581319072389e-148.22812540942476e-12
TCF12#6938184.350462914530813.01792345088513e-082.0466812161493e-06
TCF7L2#6934112.692544140784340.001864785265818270.0109994526362134
TFAP2A#7020114.129658593261244.71529045360775e-050.000824477180117763
TFAP2C#7022184.421957158579182.34378191509229e-081.64947600694288e-06
USF1#7391162.313272464439260.000684390951242380.00551946768778401
USF2#7392144.133880986158513.17273019452934e-060.000106889280253693
YY1#7528313.460143028306131.11370161383446e-121.55916733039219e-10
ZEB1#693583.070624003189790.003923162666449740.019115945960686
ZNF263#10127162.989760595276613.24708036830591e-050.000646315659587385



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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