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Coexpression cluster:C509: Difference between revisions

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{{Coexpression_clusters
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vesicle!0.0188889352968199!79666;54812$GO:0007254!JNK cascade!0.0188889352968199!51347;10746$GO:0031098!stress-activated protein kinase signaling pathway!0.0188889352968199!51347;10746$GO:0007243!protein kinase cascade!0.0188889352968199!3454;51347;10746$GO:0043687!post-translational protein modification!0.0277494551879854!81545;1540;8897;51347;10746$GO:0019962!interferon-alpha/beta binding!0.0277494551879854!3454$GO:0004905!interferon-alpha/beta receptor activity!0.0277494551879854!3454$GO:0046329!negative regulation of JNK cascade!0.0322552606000145!51347$GO:0005737!cytoplasm!0.0322552606000145!81545;1540;8897;50618;79666;51347;10746;54812$GO:0000165!MAPKKK cascade!0.0322552606000145!51347;10746$GO:0006464!protein modification process!0.0322552606000145!81545;1540;8897;51347;10746$GO:0030121!AP-1 adaptor complex!0.0322552606000145!54812$GO:0019961!interferon binding!0.0322552606000145!3454$GO:0004904!interferon receptor activity!0.0322552606000145!3454$GO:0044424!intracellular part!0.0322552606000145!81545;50618;79666;51347;1655;1540;8897;26959;54812;10746$GO:0043412!biopolymer modification!0.0322552606000145!81545;1540;8897;51347;10746$GO:0045786!negative regulation of progression through cell cycle!0.0408542297560198!1540;26959$GO:0045351!interferon type I biosynthetic process!0.0408542297560198!3454$GO:0032606!interferon type I 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48466,0.337521,0.378673,0.0101482,0.15359,0.237135,0.340182,0.109967,0.201185,0.581027,0.746375,0.0206116,0.868276,0.470823,0.600289,0.278043,0.262409,0.738063,0.787469,0.0215564,0.0331896,0.114846,0.594404,0.28079,0.208459,0.282931,0.749886,0.736358,0.148095,0.801858,0.682653,0.522191,0.185105,0.196269,0.520448,0.0107067,0.136418,0.590036,0.322755,0.0312791,0.660181,0.782075,0.445395,0.907598,0.45388,0.752806,0.0235851,0.41671,0.898367,0.677018,0.278177,0.850245,0.357633,0.849415,0.472167,0.779178,0.323245,0.0206677,0.767256,0.521666,0.749347,0.9322|tfbs_overrepresentation_for_novel_motifs=1.32905,0.0248597,1.30024,0.226461,0.336835,0.225244,0.283394,0.0452372,0.384015,1.27077,1.11118,0.318077,0.288598,0.753523,0.102247,0.370545,1.1846,0.0738698,0.315616,0.232667,0.12778,0.398767,2.58067,0.329158,0.475132,0.336616,0.0230489,0.622543,1.15013,0.0846754,1.04997,0.502277,0.212656,0.293433,1.00593,0.101974,4.04313,0.64174,0.248245,0.969099,0.283797,0.523145,0.457003,0.101392,0.222476,0.883184,0.776062,0.195517,0.133768,0.696543,1.64556,0.293583,0.145063,0.571408,0.712611,0.276665,0.107283,0.700573,0.674283,0.698795,0.538962,0.780312,0.385159,0.445454,2.25162,1.06781,0.795966,1.15172,0.493047,0.993712,1.54148,0.0475211,3.83425,0.710737,1.19751,1.52834,0.226496,0.430778,0.490165,0.152902,0.139569,0.444519,0.300103,0.0463558,0.662744,3.17665,0.229022,0.396439,0.370044,1.24919,0.885103,0.637733,0.517273,0.0617781,1.14107,0.0679169,0.132621,0.555608,1.73474,0.175673,0.25011,0.512221,1.35692,0.472938,0.405789,1.09847,1.16163,0.27168,0.474718,1.59041,0.134708,0.548062,0.392758,0.603824,0.839147,0.0817205,1.26849,0.186928,0.413654,0.490021,0.702982,0.368007,0.22321,0.309149,0.945405,0.431436,0.278404,0.521744,0.742996,0.517952,0.638371,0.555366,0.756554,0.30647,0.897471,0.0745004,0.183595,0.21836,0.856781,1.69932,1.30076,0.82115,0.27976,0.552418,0.407293,1.27096,0.393075,1.5412,0.174198,0.821735,0.691384,5.32599,0.638724,0.159909,0.285738,1.0234,0.356515,0.315972,0.156987,1.36658,0.819992,0.621644,1.22694,1.37915,0.421111,0.299472,0.20196,0.282346,0.675707|tfbs_overrepresentation_jaspar=MA0003.1;0.828137,MA0004.1;2.49239,MA0006.1;1.13118,MA0007.1;1.07281,MA0009.1;0.600198,MA0014.1;3.61289,MA0017.1;0.125342,MA0019.1;0.322194,MA0024.1;1.25925,MA0025.1;0.725013,MA0027.1;2.18072,MA0028.1;1.19395,MA0029.1;0.522011,MA0030.1;0.511665,MA0031.1;0.454061,MA0038.1;0.779114,MA0040.1;0.527306,MA0041.1;0.220669,MA0042.1;0.197306,MA0043.1;0.60049,MA0046.1;0.590147,MA0048.1;0.788745,MA0050.1;0.197941,MA0051.1;0.282227,MA0052.1;0.530811,MA0055.1;0.231394,MA0056.1;0,MA0057.1;1.42885,MA0058.1;2.68249,MA0059.1;0.140431,MA0060.1;5.95024,MA0061.1;0.585515,MA0063.1;0,MA0066.1;0.285934,MA0067.1;0.900956,MA0068.1;0.239549,MA0069.1;0.586593,MA0070.1;0.576293,MA0071.1;0.255111,MA0072.1;0.572162,MA0073.1;0.815648,MA0074.1;0.281628,MA0076.1;0.902204,MA0077.1;0.565087,MA0078.1;0.363755,MA0081.1;0.855093,MA0083.1;0.607144,MA0084.1;1.08294,MA0087.1;0.569916,MA0088.1;1.24413,MA0089.1;0,MA0090.1;0.485893,MA0091.1;0.208918,MA0092.1;0.181853,MA0093.1;2.95386,MA0095.1;0,MA0098.1;0,MA0100.1;0.296726,MA0101.1;0.343779,MA0103.1;0.320022,MA0105.1;0.970472,MA0106.1;1.54181,MA0107.1;0.871747,MA0108.2;0.451357,MA0109.1;0,MA0111.1;0.508569,MA0113.1;0.332535,MA0114.1;0.495259,MA0115.1;0.827474,MA0116.1;0.0681676,MA0117.1;0.635078,MA0119.1;0.130226,MA0122.1;1.58517,MA0124.1;0.787807,MA0125.1;0.708116,MA0130.1;0,MA0131.1;1.75293,MA0132.1;0,MA0133.1;0,MA0135.1;0.628343,MA0136.1;1.44198,MA0139.1;0.123548,MA0140.1;0.253051,MA0141.1;0.430939,MA0142.1;0.426146,MA0143.1;0.332682,MA0144.1;0.459643,MA0145.1;0.512167,MA0146.1;1.34309,MA0147.1;0.898277,MA0148.1;0.225411,MA0149.1;0.245595,MA0062.2;3.38263,MA0035.2;0.252505,MA0039.2;6.46957,MA0138.2;0.364793,MA0002.2;0.357374,MA0137.2;0.368913,MA0104.2;1.05445,MA0047.2;0.309071,MA0112.2;2.46482,MA0065.2;0.32973,MA0150.1;0.157331,MA0151.1;0,MA0152.1;0.258148,MA0153.1;0.692238,MA0154.1;1.28584,MA0155.1;0.665536,MA0156.1;0.749879,MA0157.1;0.402372,MA0158.1;0,MA0159.1;1.35392,MA0160.1;0.666979,MA0161.1;0,MA0162.1;4.02017,MA0163.1;0.839051,MA0164.1;0.342871,MA0080.2;1.14336,MA0018.2;0.85709,MA0099.2;0.258426,MA0079.2;6.90776,MA0102.2;1.11935,MA0258.1;0.436156,MA0259.1;1.92715,MA0442.1;0}}
|full_id=C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral
|id=C509
}}

Latest revision as of 11:24, 17 September 2013


Full id: C509_Neutrophils_Eosinophils_CD14_Whole_CD34_CD19_Peripheral



Phase1 CAGE Peaks

Hg19::chr10:99894399..99894453,+p1@C10orf28
Hg19::chr11:95522907..95522989,-p1@FAM76B
Hg19::chr12:105501487..105501562,+p1@KIAA1033
Hg19::chr12:118810688..118810744,-p1@TAOK3
Hg19::chr16:50775971..50776014,+p1@CYLD
Hg19::chr17:62502968..62503006,-p2@DDX5
Hg19::chr18:9137005..9137035,+p@chr18:9137005..9137035
+
Hg19::chr21:34697258..34697336,+p1@IFNAR1
Hg19::chr22:30279148..30279192,+p1@MTMR3
Hg19::chr2:128145498..128145563,-p1@MAP3K2
Hg19::chr2:24583314..24583433,-p1@ITSN2
Hg19::chr2:64751475..64751556,+p1@AFTPH
Hg19::chr5:147763539..147763586,+p1@FBXO38
Hg19::chr7:106809432..106809455,+p1@HBP1
Hg19::chr8:96145974..96146041,+p1@PLEKHF2
Hg19::chrX:100663186..100663241,+p1@HNRNPH2
Hg19::chrX:44732415..44732450,+p1@KDM6A
Hg19::chrX:54070731..54070781,-p1@PHF8


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:0030133transport vesicle0.0188889352968199
GO:0007254JNK cascade0.0188889352968199
GO:0031098stress-activated protein kinase signaling pathway0.0188889352968199
GO:0007243protein kinase cascade0.0188889352968199
GO:0043687post-translational protein modification0.0277494551879854
GO:0019962interferon-alpha/beta binding0.0277494551879854
GO:0004905interferon-alpha/beta receptor activity0.0277494551879854
GO:0046329negative regulation of JNK cascade0.0322552606000145
GO:0005737cytoplasm0.0322552606000145
GO:0000165MAPKKK cascade0.0322552606000145
GO:0006464protein modification process0.0322552606000145
GO:0030121AP-1 adaptor complex0.0322552606000145
GO:0019961interferon binding0.0322552606000145
GO:0004904interferon receptor activity0.0322552606000145
GO:0044424intracellular part0.0322552606000145
GO:0043412biopolymer modification0.0322552606000145
GO:0045786negative regulation of progression through cell cycle0.0408542297560198
GO:0045351interferon type I biosynthetic process0.0408542297560198
GO:0032606interferon type I production0.0408542297560198



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
leukocyte3.70e-47136
hematopoietic lineage restricted progenitor cell3.06e-39120
hematopoietic stem cell1.17e-38168
angioblastic mesenchymal cell1.17e-38168
nongranular leukocyte1.19e-36115
hematopoietic oligopotent progenitor cell3.91e-36161
hematopoietic multipotent progenitor cell3.91e-36161
myeloid leukocyte5.15e-3572
hematopoietic cell5.78e-34177
granulocyte monocyte progenitor cell2.68e-3167
myeloid lineage restricted progenitor cell4.31e-3066
macrophage dendritic cell progenitor2.04e-2861
defensive cell9.80e-2848
phagocyte9.80e-2848
monopoietic cell1.63e-2759
monocyte1.63e-2759
monoblast1.63e-2759
promonocyte1.63e-2759
classical monocyte8.41e-2742
CD14-positive, CD16-negative classical monocyte8.41e-2742
myeloid cell3.82e-26108
common myeloid progenitor3.82e-26108
lymphoid lineage restricted progenitor cell1.44e-0952
nucleate cell1.55e-0955
lymphocyte3.08e-0953
common lymphoid progenitor3.08e-0953
stuff accumulating cell2.45e-0887
mature alpha-beta T cell3.37e-0818
alpha-beta T cell3.37e-0818
immature T cell3.37e-0818
mature T cell3.37e-0818
immature alpha-beta T cell3.37e-0818
mesenchymal cell1.02e-07354
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.74e-3398
blood island1.74e-3398
hemolymphoid system1.73e-30108
bone marrow2.78e-2676
bone element8.26e-2582
immune system8.61e-2593
adult organism8.26e-24114
skeletal element1.12e-2190
skeletal system9.41e-20100
neural tube1.09e-0756
neural rod1.09e-0756
future spinal cord1.09e-0756
neural keel1.09e-0756
regional part of forebrain4.70e-0741
forebrain4.70e-0741
anterior neural tube4.70e-0741
future forebrain4.70e-0741
regional part of nervous system5.36e-0753
regional part of brain5.36e-0753


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)
MA0003.10.828137
MA0004.12.49239
MA0006.11.13118
MA0007.11.07281
MA0009.10.600198
MA0014.13.61289
MA0017.10.125342
MA0019.10.322194
MA0024.11.25925
MA0025.10.725013
MA0027.12.18072
MA0028.11.19395
MA0029.10.522011
MA0030.10.511665
MA0031.10.454061
MA0038.10.779114
MA0040.10.527306
MA0041.10.220669
MA0042.10.197306
MA0043.10.60049
MA0046.10.590147
MA0048.10.788745
MA0050.10.197941
MA0051.10.282227
MA0052.10.530811
MA0055.10.231394
MA0056.10
MA0057.11.42885
MA0058.12.68249
MA0059.10.140431
MA0060.15.95024
MA0061.10.585515
MA0063.10
MA0066.10.285934
MA0067.10.900956
MA0068.10.239549
MA0069.10.586593
MA0070.10.576293
MA0071.10.255111
MA0072.10.572162
MA0073.10.815648
MA0074.10.281628
MA0076.10.902204
MA0077.10.565087
MA0078.10.363755
MA0081.10.855093
MA0083.10.607144
MA0084.11.08294
MA0087.10.569916
MA0088.11.24413
MA0089.10
MA0090.10.485893
MA0091.10.208918
MA0092.10.181853
MA0093.12.95386
MA0095.10
MA0098.10
MA0100.10.296726
MA0101.10.343779
MA0103.10.320022
MA0105.10.970472
MA0106.11.54181
MA0107.10.871747
MA0108.20.451357
MA0109.10
MA0111.10.508569
MA0113.10.332535
MA0114.10.495259
MA0115.10.827474
MA0116.10.0681676
MA0117.10.635078
MA0119.10.130226
MA0122.11.58517
MA0124.10.787807
MA0125.10.708116
MA0130.10
MA0131.11.75293
MA0132.10
MA0133.10
MA0135.10.628343
MA0136.11.44198
MA0139.10.123548
MA0140.10.253051
MA0141.10.430939
MA0142.10.426146
MA0143.10.332682
MA0144.10.459643
MA0145.10.512167
MA0146.11.34309
MA0147.10.898277
MA0148.10.225411
MA0149.10.245595
MA0062.23.38263
MA0035.20.252505
MA0039.26.46957
MA0138.20.364793
MA0002.20.357374
MA0137.20.368913
MA0104.21.05445
MA0047.20.309071
MA0112.22.46482
MA0065.20.32973
MA0150.10.157331
MA0151.10
MA0152.10.258148
MA0153.10.692238
MA0154.11.28584
MA0155.10.665536
MA0156.10.749879
MA0157.10.402372
MA0158.10
MA0159.11.35392
MA0160.10.666979
MA0161.10
MA0162.14.02017
MA0163.10.839051
MA0164.10.342871
MA0080.21.14336
MA0018.20.85709
MA0099.20.258426
MA0079.26.90776
MA0102.21.11935
MA0258.10.436156
MA0259.11.92715
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#46778.735678982336747.11832414395998e-060.000205197531126425
BHLHE40#855349.971514121550540.0005867890152550460.00491567000595346
BRCA1#67255.606730734228820.00148351682127060.00948903805099707
CCNT2#905144.928156782082059.60784791139458e-097.30833232351157e-07
CHD2#1106116.321347287515861.14456586357404e-076.64096190143384e-06
E2F1#1869143.816858278239472.80080033108096e-071.41927601056654e-05
E2F4#187485.630249029015313.19335818496187e-050.000640997761828238
EBF1#187962.968822282189670.01122401152627930.0412131118304356
EGR1#1958133.602573790696212.58786130943899e-069.08788323122052e-05
ELF1#1997153.548414965672951.40980687262883e-077.9847516252973e-06
ELK4#200576.313876200515345.82725740562361e-050.000969097032143192
EP300#203383.010640767210310.002449702240952020.0137891803569466
ETS1#211394.864380461101172.6061409457402e-050.000562826208089662
FOS#235373.499204842347820.002184794619119820.0126009368912224
FOSL2#235565.643400201520560.0004238997356359670.00396237935112188
FOXA1#316974.30944101364990.0006312507809548920.00518417868303436
GABPB1#255393.533841918091090.0003266634257492130.00333005383326716
GATA1#262364.520102714600150.001371779480240890.009025278892332
GTF2B#295947.098628874294270.002064127539227270.0119710915187337
GTF2F1#296264.246553625585880.001895373487637690.011164744031325
HEY1#23462163.591209816093961.78396865355315e-081.28760125921519e-06
HMGN3#932483.634910099266930.000697360510488150.00560933721155822
HNF4A#317245.140508969545260.006558627673544430.0280325973234011
HNF4G#317457.987061812901890.0002976702118892140.00310604248771082
IRF1#3659166.788590003167918.74521507392966e-131.23759013158013e-10
IRF3#3661410.44043382477550.000493773906886250.00436694496242637
JUN#372553.475785886760090.01153499712370480.0421844514532742
JUND#3727103.885924412150575.14688713080812e-050.000876036090375602
MAX#4149134.660178978727371.17151458807717e-076.76350536562697e-06
MXI1#460194.980785814379652.15158679768434e-050.000473970836455082
MYC#4609123.48152124773961.40881703397654e-050.000338943658630444
NFE2#4778417.15650236702877.43078141794464e-050.00115142934793579
NFKB1#4790164.878278599283411.5468342524303e-101.63181638878352e-08
NFYA#480099.212790349915261.26299161532635e-077.22770308564758e-06
NFYB#480187.448797001571764.07516661513521e-060.000129521097418779
PAX5#5079124.446377020785229.8090335066856e-074.16272104999893e-05
PBX3#509056.08736463520670.00102688891506630.00727543934608296
POLR2A#5430182.147453176558071.059158074972e-064.41234185049864e-05
POU2F2#545284.047166247885570.0003333649302719250.00339472503438666
SIN3A#25942164.807897534946791.94005847662396e-102.01609718646896e-08
SIX5#14791287.594095713537333.52877746851906e-060.000116553444033732
SP1#6667103.16576743230050.0003042284203438780.00313841485502709
SP2#666857.264869581623510.0004602651152282540.00424081414815382
SPI1#668873.190570253314390.003725697551062360.0185749535294731
SREBF1#672037.834308240081380.006180412423529390.0273205829637258
TAF1#6872173.157321492092781.58473138591732e-081.16064348677292e-06
TAF7#687995.716534702461966.97179630487212e-060.000201362675410547
TBP#6908163.294907277419016.69614874550662e-084.07302899727412e-06
TCF12#693863.544821634062140.004732116341051210.0222911685780095
TCF7L2#693474.188401996775630.0007501787427136260.00590591871779499
TFAP2C#702274.203588903834530.0007339404613321410.00584416040264314
USF1#7391155.30124939767334.46175296849933e-104.35089652919796e-08
USF2#739296.49609869253482.41613336419054e-068.55095060734312e-05
YY1#7528143.819799472108552.77275053238948e-071.40642687155039e-05
ZEB1#693554.69123111598440.003248544879166750.0168282713474181
ZNF143#770286.000389578767962.00891846238146e-050.000445833904149294
ZNF263#10127104.567689798339261.21695898680601e-050.000302974921628207



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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