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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:20, 17 September 2013


Full id: C344_Neutrophils_CD14_Eosinophils_Whole_blood_CD14CD16_gall



Phase1 CAGE Peaks

Hg19::chr12:40618649..40618678,-p@chr12:40618649..40618678
-
Hg19::chr12:40618680..40618710,-p@chr12:40618680..40618710
-
Hg19::chr14:95652006..95652032,+p@chr14:95652006..95652032
+
Hg19::chr15:45018966..45018983,-p@chr15:45018966..45018983
-
Hg19::chr15:45019081..45019115,+p@chr15:45019081..45019115
+
Hg19::chr15:55581954..55582018,-p1@RAB27A
Hg19::chr15:86087074..86087082,+p48@AKAP13
Hg19::chr15:86087098..86087118,+p12@AKAP13
Hg19::chr15:86087125..86087141,+p18@AKAP13
Hg19::chr16:74734672..74734722,-p2@MLKL
Hg19::chr17:76384663..76384707,-p@chr17:76384663..76384707
-
Hg19::chr17:76409198..76409218,-p@chr17:76409198..76409218
-
Hg19::chr17:76413038..76413051,-p@chr17:76413038..76413051
-
Hg19::chr19:1132472..1132486,+p@chr19:1132472..1132486
+
Hg19::chr1:154580616..154580695,-p1@ADAR
Hg19::chr1:221054774..221054789,-p@chr1:221054774..221054789
-
Hg19::chr1:245214949..245214973,+p@chr1:245214949..245214973
+
Hg19::chr1:28270172..28270184,+p@chr1:28270172..28270184
+
Hg19::chr1:40840377..40840413,+p7@SMAP2
Hg19::chr20:3993560..3993585,+p@chr20:3993560..3993585
+
Hg19::chr20:48909087..48909099,-p@chr20:48909087..48909099
-
Hg19::chr21:34602680..34602705,+p4@IFNAR2
Hg19::chr22:31626561..31626578,-p4@ENST00000365149
Hg19::chr2:152146385..152146435,-p2@NMI
Hg19::chr3:187463154..187463172,-p@chr3:187463154..187463172
-
Hg19::chr3:46150615..46150632,+p@chr3:46150615..46150632
+
Hg19::chr4:15661474..15661499,-p5@FBXL5
Hg19::chr7:134832793..134832807,+p3@TMEM140
Hg19::chr7:134832808..134832879,+p1@TMEM140
Hg19::chr9:114423841..114423900,+p1@GNG10
Hg19::chrX:12924732..12924745,+p1@TLR8
Hg19::chrX:12924771..12924776,+p2@TLR8
Hg19::chrX:48554974..48554979,-p@chrX:48554974..48554979
-


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:0007259JAK-STAT cascade0.00887448671705014
GO:0003725double-stranded RNA binding0.00887448671705014
GO:0007242intracellular signaling cascade0.00887448671705014
GO:0007243protein kinase cascade0.00887448671705014
GO:0009615response to virus0.0149020786189561
GO:0019962interferon-alpha/beta binding0.0149020786189561
GO:0004905interferon-alpha/beta receptor activity0.0149020786189561
GO:0005121Toll binding0.0149020786189561
GO:0003726double-stranded RNA adenosine deaminase activity0.0149020786189561
GO:0009597detection of virus0.0149020786189561
GO:0045359positive regulation of interferon-beta biosynthetic process0.0149020786189561
GO:0032608interferon-beta production0.0149020786189561
GO:0045357regulation of interferon-beta biosynthetic process0.0149020786189561
GO:0016553base conversion or substitution editing0.0149020786189561
GO:0003969RNA editase activity0.0149020786189561
GO:0045356positive regulation of interferon-alpha biosynthetic process0.0149020786189561
GO:0045350interferon-beta biosynthetic process0.0149020786189561
GO:0007165signal transduction0.0149020786189561
GO:0045354regulation of interferon-alpha biosynthetic process0.0149020786189561
GO:0019961interferon binding0.0149020786189561
GO:0032607interferon-alpha production0.0149020786189561
GO:0045349interferon-alpha biosynthetic process0.0149020786189561
GO:0004904interferon receptor activity0.0149020786189561
GO:0051707response to other organism0.0154822736543798
GO:0045416positive regulation of interleukin-8 biosynthetic process0.0164497156937845
GO:0007154cell communication0.0182726205744676
GO:0032606interferon type I production0.0182726205744676
GO:0045414regulation of interleukin-8 biosynthetic process0.0182726205744676
GO:0004691cAMP-dependent protein kinase activity0.0182726205744676
GO:0045351interferon type I biosynthetic process0.0182726205744676
GO:0042228interleukin-8 biosynthetic process0.0198275305357204
GO:0003924GTPase activity0.0198275305357204
GO:0045078positive regulation of interferon-gamma biosynthetic process0.0198275305357204
GO:0045089positive regulation of innate immune response0.0198275305357204
GO:0009607response to biotic stimulus0.0198275305357204
GO:0006954inflammatory response0.0198275305357204
GO:0032637interleukin-8 production0.0198275305357204
GO:0045088regulation of innate immune response0.0198275305357204
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0200446930089062
GO:0045072regulation of interferon-gamma biosynthetic process0.0200446930089062
GO:0031047RNA-mediated gene silencing0.0200446930089062
GO:0042095interferon-gamma biosynthetic process0.0211952510192287
GO:0051704multi-organism process0.021785239839871
GO:0009595detection of biotic stimulus0.021785239839871
GO:0004000adenosine deaminase activity0.023808613748567
GO:0051607defense response to virus0.023808613748567
GO:0032609interferon-gamma production0.0262078614030427
GO:0003727single-stranded RNA binding0.0285056322417812
GO:0009611response to wounding0.0309794943871959
GO:0005834heterotrimeric G-protein complex0.0498755017895259
GO:0030425dendrite0.0498755017895259
GO:0016458gene silencing0.0498755017895259



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
myeloid leukocyte2.39e-7472
defensive cell1.65e-7248
phagocyte1.65e-7248
classical monocyte9.71e-6842
CD14-positive, CD16-negative classical monocyte9.71e-6842
monopoietic cell3.24e-6559
monocyte3.24e-6559
monoblast3.24e-6559
promonocyte3.24e-6559
macrophage dendritic cell progenitor1.52e-6261
myeloid lineage restricted progenitor cell1.06e-5866
granulocyte monocyte progenitor cell1.41e-5767
leukocyte3.76e-49136
nongranular leukocyte2.89e-44115
myeloid cell3.45e-43108
common myeloid progenitor3.45e-43108
hematopoietic lineage restricted progenitor cell4.34e-38120
hematopoietic stem cell8.39e-37168
angioblastic mesenchymal cell8.39e-37168
hematopoietic oligopotent progenitor cell5.57e-34161
hematopoietic multipotent progenitor cell5.57e-34161
hematopoietic cell8.26e-34177
stuff accumulating cell9.12e-3387
intermediate monocyte1.47e-149
CD14-positive, CD16-positive monocyte1.47e-149
granulocyte1.57e-148
blood cell4.90e-1011
mesenchymal cell5.15e-07354
neutrophil5.79e-073
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.49e-6898
blood island2.49e-6898
hemolymphoid system3.88e-64108
bone marrow8.57e-5176
immune system5.29e-4993
bone element7.74e-4682
skeletal element2.91e-4090
skeletal system1.46e-34100
lateral plate mesoderm9.99e-26203
blood1.02e-1515
haemolymphatic fluid1.02e-1515
organism substance1.02e-1515
adult organism5.12e-15114
musculoskeletal system2.36e-14167
mesoderm3.58e-13315
mesoderm-derived structure3.58e-13315
presumptive mesoderm3.58e-13315


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)
MA0003.10.122744
MA0004.10.080382
MA0006.10.490695
MA0007.10.0722718
MA0009.10.385713
MA0014.10.214829
MA0017.10.332079
MA0019.10.930329
MA0024.10.303271
MA0025.10.497679
MA0027.11.91867
MA0028.10.290206
MA0029.10.318031
MA0030.10.832636
MA0031.12.86451
MA0038.10.41263
MA0040.10.322542
MA0041.12.11185
MA0042.11.93339
MA0043.11.00296
MA0046.10.376892
MA0048.10.8556
MA0050.13.18558
MA0051.13.29093
MA0052.10.869177
MA0055.10.942187
MA0056.10
MA0057.10.0145285
MA0058.10.0435692
MA0059.10.165985
MA0060.10.20893
MA0061.10.070207
MA0063.10
MA0066.10.413239
MA0067.10.661236
MA0068.10.0982234
MA0069.10.373781
MA0070.10.364788
MA0071.10.111216
MA0072.10.361192
MA0073.10.0224344
MA0074.10.129338
MA0076.10.724617
MA0077.10.355047
MA0078.10.189533
MA0081.10.377736
MA0083.10.391829
MA0084.10.834984
MA0087.10.359239
MA0088.10.0584509
MA0089.10
MA0090.10.0540248
MA0091.10.278484
MA0092.10.232971
MA0093.10.0261504
MA0095.10
MA0098.10
MA0100.10.432601
MA0101.10.113129
MA0103.10.465544
MA0105.10.0309513
MA0106.10.156032
MA0107.10.15894
MA0108.20.259018
MA0109.10
MA0111.10.21427
MA0113.10.165999
MA0114.10.152032
MA0115.10.592273
MA0116.10.326698
MA0117.10.416571
MA0119.10.0381354
MA0122.11.11659
MA0124.10.555413
MA0125.10.482287
MA0130.10
MA0131.11.73378
MA0132.10
MA0133.10
MA0135.10.410584
MA0136.10.835939
MA0139.10.423475
MA0140.10.10984
MA0141.10.0425918
MA0142.10.238557
MA0143.10.166108
MA0144.11.77852
MA0145.10.482648
MA0146.10.0133414
MA0147.10.0133837
MA0148.11.06077
MA0149.11.15093
MA0062.20.451147
MA0035.20.353942
MA0039.20.0161386
MA0138.20.556703
MA0002.20.0282628
MA0137.21.7091
MA0104.20.00601882
MA0047.22.05733
MA0112.20.305716
MA0065.20.14488
MA0150.10.750979
MA0151.10
MA0152.10.363874
MA0153.10.467885
MA0154.10.0292415
MA0155.10.400182
MA0156.11.7238
MA0157.11.83312
MA0158.10
MA0159.10.0134864
MA0160.10.0992022
MA0161.10
MA0162.10.152257
MA0163.10.237378
MA0164.10.516398
MA0080.21.58444
MA0018.20.156863
MA0099.20.364364
MA0079.20.000216428
MA0102.20.870137
MA0258.10.6811
MA0259.10.355499
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
BATF#1053853.690576029136910.01058778017317130.0391024142828895
BRF2#55290265.12579281183930.0004460473776813310.00415193779658293
CEBPB#1051143.381698992774161.86072005286264e-050.000422644066117705
CTCF#10664121.949184135663650.01269333499092020.0457999382662539
EP300#2033122.463251536808440.001814354306423650.0108989617743345
FOXA1#3169113.693806583128489.47506033378001e-050.00137325260366313
FOXA2#317075.224643826322930.0003049755240633990.00314581123532418
GTF2F1#296272.702352307191020.0127138666355930.0458676817007393
HDAC2#306683.252271572515460.002431075584245950.0136931885957859
HNF4A#317253.504892479235410.01302613334164830.046218323087087
HNF4G#317454.356579170673760.0053489529933270.0245739366414498
JUNB#372665.565569574512930.0006282293092728520.00516993466481344
MAFF#23764711.94568167968531.5762538789157e-066.00154498213915e-05
MAFK#797597.391109037589982.17305616749095e-067.82053111911051e-05
MAX#4149112.150851836335710.008663849095600580.0329753547993961
MEF2A#420563.407860165389830.007343856569733540.0303672263644297
RXRA#625663.649930388933320.005286747489684540.0244841745853915
SPI1#6688122.983390366735540.0003176219983968550.00325312581058833
STAT1#6772127.52966818079972.18515375642827e-081.54722219096686e-06
STAT2#6773917.79921032357471.27255403713315e-091.15468523965377e-07
STAT3#6774165.10034666528691.05453466606223e-087.94621543931266e-07
TAL1#688654.525547981430330.004558483051493650.0215461355636742



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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