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Coexpression cluster:C280: Difference between revisions

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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:12, 17 September 2013


Full id: C280_Mast_Natural_CD19_CD8_Eosinophils_CD34_CD4



Phase1 CAGE Peaks

Hg19::chr10:3827417..3827428,-p3@KLF6
Hg19::chr11:62323018..62323031,-p@chr11:62323018..62323031
-
Hg19::chr11:65657918..65657945,-p@chr11:65657918..65657945
-
Hg19::chr11:66610757..66610775,-p3@CU688443
Hg19::chr12:25539082..25539099,-p@chr12:25539082..25539099
-
Hg19::chr12:9913489..9913506,-p1@CD69
Hg19::chr14:105947382..105947418,+p@chr14:105947382..105947418
+
Hg19::chr14:105947980..105947997,-p@chr14:105947980..105947997
-
Hg19::chr14:60715694..60715716,-p1@ENST00000529171
Hg19::chr14:75725656..75725708,-p@chr14:75725656..75725708
-
Hg19::chr14:75761343..75761358,+p@chr14:75761343..75761358
+
Hg19::chr17:17586443..17586462,-p@chr17:17586443..17586462
-
Hg19::chr17:17739693..17739737,+p@chr17:17739693..17739737
+
Hg19::chr17:38478879..38478895,-p@chr17:38478879..38478895
-
Hg19::chr17:62972061..62972090,-p7@AMZ2P1
Hg19::chr19:14117737..14117757,+p@chr19:14117737..14117757
+
Hg19::chr19:39892410..39892428,+p@chr19:39892410..39892428
+
Hg19::chr19:39892441..39892455,+p@chr19:39892441..39892455
+
Hg19::chr19:45954222..45954237,+p@chr19:45954222..45954237
+
Hg19::chr19:45954249..45954276,+p@chr19:45954249..45954276
+
Hg19::chr19:45954279..45954294,+p@chr19:45954279..45954294
+
Hg19::chr19:45972701..45972774,+p2@FOSB
Hg19::chr19:50554282..50554297,-p@chr19:50554282..50554297
-
Hg19::chr19:58609835..58609860,+p@chr19:58609835..58609860
+
Hg19::chr1:150207241..150207263,+p@chr1:150207241..150207263
+
Hg19::chr1:150584212..150584225,+p@chr1:150584212..150584225
+
Hg19::chr1:156076042..156076062,-p@chr1:156076042..156076062
-
Hg19::chr1:171455188..171455201,-p3@BC007549
Hg19::chr1:19923143..19923206,-p1@ENST00000416470
Hg19::chr1:245132972..245133020,+p2@EFCAB2
Hg19::chr1:245133062..245133098,+p3@EFCAB2
Hg19::chr20:34384518..34384529,-p@chr20:34384518..34384529
-
Hg19::chr21:44847380..44847401,+p@chr21:44847380..44847401
+
Hg19::chr22:42078575..42078594,+p@chr22:42078575..42078594
+
Hg19::chr2:157189859..157189868,+p@chr2:157189859..157189868
+
Hg19::chr2:201729344..201729359,-p3@CLK1
Hg19::chr2:24149009..24149030,+p@chr2:24149009..24149030
+
Hg19::chr2:25195035..25195063,+p2@DNAJC27-AS1
Hg19::chr3:20227985..20227998,+p@chr3:20227985..20227998
+
Hg19::chr6:116575441..116575452,+p4@uc003pwo.1
Hg19::chr6:157342586..157342600,-p@chr6:157342586..157342600
-
Hg19::chr6:16129308..16129327,+p1@MYLIP
Hg19::chr8:101964446..101964498,+p@chr8:101964446..101964498
+
Hg19::chr9:3525727..3525828,-p2@RFX3
Hg19::chr9:3526503..3526519,+p2@ENST00000423112
Hg19::chr9:91933575..91933588,-p@chr9:91933575..91933588
-


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
6.17544927282532e-060.003909059389698423162TNF alpha/NF-kB down reg. targets (Netpath):NetPath_9



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

No GOStat results

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
leukocyte3.85e-66136
hematopoietic stem cell6.94e-55168
angioblastic mesenchymal cell6.94e-55168
hematopoietic lineage restricted progenitor cell4.20e-54120
nongranular leukocyte6.62e-54115
hematopoietic cell2.77e-52177
hematopoietic oligopotent progenitor cell4.48e-50161
hematopoietic multipotent progenitor cell4.48e-50161
classical monocyte3.47e-4042
CD14-positive, CD16-negative classical monocyte3.47e-4042
myeloid leukocyte1.76e-3372
defensive cell5.23e-3348
phagocyte5.23e-3348
granulocyte monocyte progenitor cell4.79e-3067
macrophage dendritic cell progenitor1.51e-2761
myeloid lineage restricted progenitor cell3.94e-2666
monopoietic cell8.39e-2659
monocyte8.39e-2659
monoblast8.39e-2659
promonocyte8.39e-2659
myeloid cell6.50e-25108
common myeloid progenitor6.50e-25108
lymphoid lineage restricted progenitor cell1.40e-2452
lymphocyte7.87e-2453
common lymphoid progenitor7.87e-2453
nucleate cell2.03e-2255
mesenchymal cell2.30e-20354
connective tissue cell1.13e-19361
motile cell7.26e-17386
stuff accumulating cell1.74e-1487
T cell3.12e-1425
pro-T cell3.12e-1425
mature alpha-beta T cell1.75e-1318
alpha-beta T cell1.75e-1318
immature T cell1.75e-1318
mature T cell1.75e-1318
immature alpha-beta T cell1.75e-1318
stem cell2.33e-12441
multi fate stem cell5.11e-12427
somatic stem cell1.07e-11433
intermediate monocyte1.27e-109
CD14-positive, CD16-positive monocyte1.27e-109
B cell7.68e-0914
lymphocyte of B lineage7.71e-0924
pro-B cell7.71e-0924
CD8-positive, alpha-beta T cell2.46e-0811
CD4-positive, alpha-beta T cell3.81e-086
granulocyte1.57e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.32e-3298
blood island2.32e-3298
bone marrow5.34e-2876
hemolymphoid system3.60e-27108
bone element1.03e-2582
immune system2.89e-2393
skeletal element1.44e-2290
skeletal system1.99e-18100
connective tissue4.58e-18371
lateral plate mesoderm2.25e-08203


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)
MA0003.11.54111
MA0004.10.623722
MA0006.11.29286
MA0007.10.314162
MA0009.10.771045
MA0014.14.64327
MA0017.10.0615642
MA0019.11.06433
MA0024.10.603486
MA0025.10.383675
MA0027.11.77546
MA0028.10.27871
MA0029.10.633517
MA0030.10.615653
MA0031.10.174316
MA0038.10.0730457
MA0040.10.226506
MA0041.10.0434336
MA0042.10.138038
MA0043.10.771566
MA0046.10.274202
MA0048.10.477418
MA0050.11.33029
MA0051.10.533459
MA0052.10.648779
MA0055.10.484343
MA0056.10
MA0057.11.20269
MA0058.10.633056
MA0059.10.19517
MA0060.11.09139
MA0061.11.43088
MA0063.10
MA0066.10.255112
MA0067.11.32821
MA0068.10.616302
MA0069.10.271442
MA0070.10.263481
MA0071.10.0583578
MA0072.10.260306
MA0073.120.5693
MA0074.10.531919
MA0076.10.686843
MA0077.10.254892
MA0078.10.116238
MA0081.10.629296
MA0083.10.287504
MA0084.10.703837
MA0087.10.717287
MA0088.10.589119
MA0089.10
MA0090.10.736947
MA0091.10.15216
MA0092.10.287028
MA0093.10.440019
MA0095.10
MA0098.10
MA0100.11.44145
MA0101.12.14905
MA0103.10.0378098
MA0105.11.27179
MA0106.10.0905927
MA0107.12.27063
MA0108.20.513366
MA0109.10
MA0111.10.107174
MA0113.10.0981023
MA0114.10.0167868
MA0115.10.471806
MA0116.10.261874
MA0117.10.83365
MA0119.10.173853
MA0122.10.329219
MA0124.10.437263
MA0125.10.36951
MA0130.10
MA0131.11.86814
MA0132.10
MA0133.10
MA0135.10.304312
MA0136.10.556727
MA0139.10.585192
MA0140.10.0574137
MA0141.10.622968
MA0142.10.155551
MA0143.10.0981847
MA0144.10.54022
MA0145.10.880308
MA0146.11.13888
MA0147.10.658893
MA0148.10.0453767
MA0149.10.0540502
MA0062.21.09443
MA0035.20.208625
MA0039.23.46483
MA0138.20.11686
MA0002.20.367496
MA0137.20.498579
MA0104.21.08539
MA0047.20.0852269
MA0112.21.66249
MA0065.20.435037
MA0150.10.716372
MA0151.10
MA0152.10.059761
MA0153.10.356306
MA0154.10.158266
MA0155.10.732376
MA0156.10.505588
MA0157.10.140121
MA0158.10
MA0159.10.444017
MA0160.10.187803
MA0161.10
MA0162.12.17126
MA0163.12.10734
MA0164.10.339401
MA0080.20.121711
MA0018.26.69118
MA0099.20.216674
MA0079.215.0938
MA0102.20.737926
MA0258.10.71509
MA0259.11.28235
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
BCL11A#5333574.317090994027160.001078084552234020.00761182210321585
BCL3#60264.506143843965870.002035986867553540.011824960096787
BRCA1#672146.143026717502882.82527442542498e-081.92603678666423e-06
CCNT2#905283.856818351194655.0761257913336e-126.61854558702984e-10
CEBPB#1051162.772573087243418.85618406965618e-050.00129760242431372
CHD2#1106184.047661109002251.04787550155742e-076.1241784838923e-06
E2F1#1869282.98710647862222.49079647788142e-092.11149588760923e-07
E2F4#1874143.855496617695277.64706218551962e-060.000217972578491671
E2F6#1876293.162989483026612.2426729101714e-102.30307292099696e-08
EBF1#1879142.710663822868830.0003629593213753860.0036243530514508
EGR1#1958333.57847630714645.64412029062498e-149.12486500050436e-12
ELF1#1997292.684453060987361.25513880516566e-089.32328888141514e-07
ELK4#200582.823596810168350.00656760806232610.0280698321501586
EP300#2033223.239711260367621.08793059315116e-076.34053477779654e-06
ESR1#2099106.688826803511841.82003034097748e-066.75487380175364e-05
FOS#2353132.54290041338320.001148129041516760.00785313045824668
FOSL2#2355124.416574070755221.05147803526648e-050.000273172424192028
FOXA1#3169122.89080515201360.0006072653966565240.00506890910816901
GABPB1#2553162.45832481258510.0003656422386977120.00364939886920397
GATA1#2623113.242682382213150.0004130141450732380.00393386085702726
GATA3#262574.144687271748740.001363545100422790.00897506061278478
GTF2B#295953.472155427643940.01418348431271470.0497584453522206
GTF2F1#2962154.154237242420971.27657572022556e-065.10625398868776e-05
HDAC2#306692.624795263687750.006228743151318980.0274888529888275
HEY1#23462332.898340530923662.79057128948827e-113.26365593396266e-09
HMGN3#9324223.911479345950283.33656122442016e-092.75468077246812e-07
HSF1#3297310.71460869565220.002809367600468750.0153801720828933
IRF1#3659203.320505979810393.90366729260953e-071.8980219197991e-05
JUN#3725143.808252362884978.80966587461091e-060.000237744882242504
JUND#3727223.345274059155716.07520271249101e-083.7677440385383e-06
MAX#4149192.665185971111642.38683755310401e-050.000520415296886493
MEF2A#4205104.074615415140010.0001287480981055410.00171116347900797
MEF2C#420854.490364618763480.004985557797800120.0232740332042038
MXI1#4601255.41389762432578.99596347527704e-141.41495395993141e-11
MYC#4609262.951724536127052.08087698330037e-081.48041356443397e-06
NFKB1#4790293.459866071774372.34035757418545e-112.787053645272e-09
NFYA#480093.605004919532060.000718040202295040.00573679625822304
NFYB#4801114.00777664758486.43485465705113e-050.00104696959889042
NR3C1#2908113.580505579193550.0001753344960213330.00213249789565297
NRF1#4899143.716172005825061.1653236447232e-050.000296552719618046
PAX5#5079273.914744985691331.19828201832722e-111.48984971085805e-09
PBX3#509094.287622047406460.0002024221915653560.00240427286078633
POLR2A#5430442.05408564714257.59234119205233e-131.08919851889664e-10
POU2F2#5452265.146939684810996.7909221724601e-141.08446042931125e-11
PRDM1#63938.597671028964830.005186038749451220.0240369547310139
RDBP#7936310.01989591239290.003389725380753140.0173004705585925
REST#5978142.936965261430270.0001564490576728030.00197287891020163
RFX5#5993236.023955413597551.67009377927883e-132.55004275166816e-11
RXRA#6256104.364047204159417.30215440325001e-050.0011468115845429
SIN3A#25942313.645117968071074.95966755376827e-137.23439552581012e-11
SMARCB1#659883.174385353244770.003254179262548840.0168566227557454
SMARCC1#659954.746017317351250.003950573519571360.0189654768012187
SP1#6667303.716335681396241.06920996712667e-121.50090349135406e-10
SP2#666863.411330064414520.007867546284875830.0323024989757498
SREBF1#672099.196796629660754.7861079389151e-072.25770698749934e-05
SRF#6722123.599263894478567.89027074196385e-050.00120899645836262
TAF1#6872423.052346608723963.92905562788341e-188.7307795897982e-16
TAF7#6879194.72235475420773.1362546328173e-092.61828375377143e-07
TBP#6908383.062114915427455.39932691943666e-159.47731603595034e-13
TCF12#6938153.467760294191221.18181286891873e-050.000299000373587701
TCF7L2#6934173.980282642898583.48856912736139e-071.72429091856364e-05
TFAP2C#7022112.584815537140490.002652407479740160.0146398258522663
USF1#7391172.350988863315980.0003775083617368490.00374457173439403
YY1#7528293.09617286403833.81833363335084e-103.78351941492911e-08
ZBTB33#1000964.130181525649720.003137552918294680.0164739273658327
ZBTB7A#51341152.39736173082910.000786133556522270.00615880297874348



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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