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{{Coexpression_clusters
{
|full_id=C325_Mast_Eosinophils_CD14_immature_Basophils_granulocyte_Natural

Latest revision as of 11:20, 17 September 2013


Full id: C325_Mast_Eosinophils_CD14_immature_Basophils_granulocyte_Natural



Phase1 CAGE Peaks

Hg19::chr10:104154139..104154150,-p@chr10:104154139..104154150
-
Hg19::chr10:134210589..134210633,-p@chr10:134210589..134210633
-
Hg19::chr11:2950407..2950420,+p1@CU674966
Hg19::chr12:52401484..52401505,-p1@GRASPOS
Hg19::chr14:105947724..105947752,-p@chr14:105947724..105947752
-
Hg19::chr14:35874235..35874259,+p@chr14:35874235..35874259
+
Hg19::chr14:75725434..75725447,-p@chr14:75725434..75725447
-
Hg19::chr14:75743997..75744000,+p@chr14:75743997..75744000
+
Hg19::chr15:66084869..66084922,+p@chr15:66084869..66084922
+
Hg19::chr17:38476670..38476683,+p@chr17:38476670..38476683
+
Hg19::chr19:12901145..12901178,+p@chr19:12901145..12901178
+
Hg19::chr19:13951731..13951736,-p@chr19:13951731..13951736
-
Hg19::chr19:13953708..13953767,-p@chr19:13953708..13953767
-
Hg19::chr19:13953876..13953941,+p@chr19:13953876..13953941
+
Hg19::chr19:13958611..13958627,-p@chr19:13958611..13958627
-
Hg19::chr19:39894385..39894411,-p@chr19:39894385..39894411
-
Hg19::chr19:45971134..45971154,-p@chr19:45971134..45971154
-
Hg19::chr19:49377375..49377386,+p@chr19:49377375..49377386
+
Hg19::chr19:54369752..54369762,+p@chr19:54369752..54369762
+
Hg19::chr1:150207079..150207107,+p@chr1:150207079..150207107
+
Hg19::chr1:150584230..150584233,+p@chr1:150584230..150584233
+
Hg19::chr1:150584237..150584248,+p@chr1:150584237..150584248
+
Hg19::chr1:150592664..150592667,+p@chr1:150592664..150592667
+
Hg19::chr1:15736145..15736158,+p7@EFHD2
Hg19::chr1:204381380..204381396,+p@chr1:204381380..204381396
+
Hg19::chr1:31229849..31229861,+p@chr1:31229849..31229861
+
Hg19::chr20:4795315..4795333,-p@chr20:4795315..4795333
-
Hg19::chr2:208031064..208031075,+p@chr2:208031064..208031075
+
Hg19::chr2:208031099..208031115,+p@chr2:208031099..208031115
+
Hg19::chr2:208394310..208394342,-p@chr2:208394310..208394342
-
Hg19::chr3:5020501..5020514,-p@chr3:5020501..5020514
-
Hg19::chr5:10564274..10564287,-p@chr5:10564274..10564287
-
Hg19::chr5:150465212..150465229,+p@chr5:150465212..150465229
+
Hg19::chr5:56469296..56469320,-p@chr5:56469296..56469320
-
Hg19::chr8:103819252..103819272,+p1@ENST00000405813
p1@ENST00000517910
p1@uc003ykw.1


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

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
classical monocyte1.44e-7942
CD14-positive, CD16-negative classical monocyte1.44e-7942
leukocyte5.04e-71136
myeloid leukocyte8.51e-7172
defensive cell6.18e-6848
phagocyte6.18e-6848
granulocyte monocyte progenitor cell1.97e-6067
macrophage dendritic cell progenitor8.67e-5861
myeloid lineage restricted progenitor cell6.42e-5666
hematopoietic stem cell1.86e-55168
angioblastic mesenchymal cell1.86e-55168
monopoietic cell2.50e-5459
monocyte2.50e-5459
monoblast2.50e-5459
promonocyte2.50e-5459
hematopoietic lineage restricted progenitor cell4.87e-54120
nongranular leukocyte2.28e-52115
hematopoietic cell1.32e-51177
hematopoietic oligopotent progenitor cell6.18e-48161
hematopoietic multipotent progenitor cell6.18e-48161
myeloid cell5.84e-46108
common myeloid progenitor5.84e-46108
stuff accumulating cell9.21e-3987
mesenchymal cell4.19e-21354
connective tissue cell2.75e-20361
intermediate monocyte5.52e-189
CD14-positive, CD16-positive monocyte5.52e-189
motile cell2.04e-17386
stem cell7.39e-15441
granulocyte5.35e-148
multi fate stem cell6.28e-14427
somatic stem cell1.89e-13433
blood cell8.60e-1011
basophil8.57e-083
natural killer cell1.14e-073
pro-NK cell1.14e-073
single nucleate cell3.93e-073
mononuclear cell3.93e-073
Uber Anatomy
Ontology termp-valuen
bone marrow4.49e-5476
hematopoietic system1.34e-5298
blood island1.34e-5298
bone element4.51e-4982
hemolymphoid system3.02e-46108
immune system3.15e-4593
skeletal element1.94e-4390
skeletal system1.15e-37100
lateral plate mesoderm6.62e-20203
connective tissue3.57e-19371
musculoskeletal system5.48e-17167
mesoderm4.74e-08315
mesoderm-derived structure4.74e-08315
presumptive mesoderm4.74e-08315


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)
MA0003.110.4784
MA0004.10.0714537
MA0006.10.441316
MA0007.11.2868
MA0009.10.960157
MA0014.13.55179
MA0017.10.2976
MA0019.10.446088
MA0024.11.42187
MA0025.10.47683
MA0027.11.89328
MA0028.10.258143
MA0029.10.30014
MA0030.10.79265
MA0031.10.685216
MA0038.10.120244
MA0040.10.304553
MA0041.10.0793669
MA0042.10.065999
MA0043.10.366755
MA0046.10.357837
MA0048.10.746574
MA0050.10.23549
MA0051.10.118004
MA0052.11.5006
MA0055.10.180482
MA0056.10
MA0057.12.09846
MA0058.10.0375298
MA0059.10.146942
MA0060.10.519009
MA0061.111.2185
MA0063.10
MA0066.13.17419
MA0067.11.54245
MA0068.14.4041
MA0069.10.354782
MA0070.10.345954
MA0071.10.100424
MA0072.10.342425
MA0073.13.96271
MA0074.11.23517
MA0076.10.042375
MA0077.10.893427
MA0078.10.175262
MA0081.10.615436
MA0083.10.973401
MA0084.10.811454
MA0087.10.340509
MA0088.11.26094
MA0089.10
MA0090.10.178129
MA0091.10.918907
MA0092.10.460323
MA0093.10.0954868
MA0095.10
MA0098.10
MA0100.10.127731
MA0101.110.1284
MA0103.10.0863031
MA0105.17.86345
MA0106.10.440452
MA0107.113.1265
MA0108.21.26212
MA0109.10
MA0111.10.749266
MA0113.10.152632
MA0114.10.26818
MA0115.10.570409
MA0116.11.42387
MA0117.10.396851
MA0119.10.898554
MA0122.10.418111
MA0124.10.533912
MA0125.10.461632
MA0130.10
MA0131.10.186723
MA0132.10
MA0133.10
MA0135.10.390959
MA0136.10.391883
MA0139.10.79031
MA0140.10.0991227
MA0141.10.0366436
MA0142.10.222682
MA0143.10.464654
MA0144.10.932046
MA0145.12.33719
MA0146.12.84201
MA0147.10.50292
MA0148.10.588112
MA0149.10.0944562
MA0062.20.392353
MA0035.20.0987789
MA0039.23.07549
MA0138.20.176028
MA0002.20.291191
MA0137.20.268939
MA0104.20.757404
MA0047.20.422993
MA0112.22.89159
MA0065.20.291442
MA0150.10.389152
MA0151.10
MA0152.10.102351
MA0153.10.447419
MA0154.11.85075
MA0155.11.77954
MA0156.10.272778
MA0157.11.11527
MA0158.10
MA0159.11.86395
MA0160.10.299258
MA0161.10
MA0162.11.89077
MA0163.17.05656
MA0164.10.160035
MA0080.20.729075
MA0018.20.869357
MA0099.21.66743
MA0079.219.7143
MA0102.20.846442
MA0258.12.39182
MA0259.10.156252
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#1053853.479685970329090.0135390230098880.0477961744229884
BCL11A#5333586.484446880824472.37869370682523e-050.000518747947477804
BCL3#60287.896480640854475.73291622041024e-060.000172299291264295
CCNT2#905152.715514961555410.0001269208423535120.00168881205944177
CEBPB#1051122.732964900282790.0007687652737523420.00603133086128462
E2F1#1869202.804222408502471.97000314401587e-067.23181575950346e-05
E2F6#1876202.866946132398511.36818304650281e-065.32780272907186e-05
EBF1#1879112.799175294635970.001130672602793560.00775048017610636
EGR1#1958202.850388054177221.50552534942405e-065.79991006892284e-05
ELF1#1997192.311538891924098.13984845356604e-050.00123312682425585
EP300#2033163.096659074844891.2218350970467e-050.000304043925900548
ETS1#211392.501681379994890.00752738959766980.0310352154352784
FOS#2353112.827928811366810.001038395056170170.0073430117998075
FOXA1#3169123.799343914075013.32893352467969e-050.000661347704744193
FOXA2#317064.222365214742610.002630116711677290.0145398453975685
GATA1#262383.099499004297240.003376243928986140.0172426180782094
GTF2F1#296282.911922486116030.004941085120141420.0230880939941144
HEY1#23462192.193203137685960.0001728615492365290.00210487202293504
HMGN3#9324133.037746297244510.0001450387852618280.00188615436358611
HNF4G#317454.10763178949240.006909545356628830.0292570852422849
IRF1#3659112.40025146540580.003915598881104370.0190799809426426
JUN#3725113.932603460448565.76961075250762e-050.000961653969647532
JUND#3727173.397408200337361.46551369536671e-065.66667104148107e-05
MAFF#2376446.436040741708020.003350442598259530.0173037718583537
MEF2A#420594.819687948194186.92480820486513e-050.00109945278824553
MEF2C#420855.901622070374860.001469732643616150.00940720767093381
MXI1#4601102.846163322502660.001791625368205810.0109893440905648
NFKB1#4790223.449639866636126.63602208945163e-095.21489474040812e-07
NR3C1#290883.422405332839550.001816942426474210.0109019677167954
PAX5#5079152.858385227647646.96946010462861e-050.0011050302776185
POLR2A#5430332.024741566469041.98434494132616e-091.71275207708399e-07
POU2F2#5452153.902624596175371.51738665994975e-065.83914316059291e-05
REST#5978113.032866167925950.0005752035764000270.0048560089172777
RFX5#5993103.442260236341460.0004074633646526460.00388559773018241
SIN3A#25942182.781712145219211.11282038498347e-050.000284857471047277
SIRT6#51548313.16900605628790.001541125096164720.00979632160184706
SMARCB1#659873.650543156231480.002556325547915270.0141438908613436
SMARCC1#659944.990098207957880.008170057913538130.0322586170062383
SMARCC2#660138.070460665162650.00607679039766490.0268818633716686
SP1#6667162.604974344292980.0001090079980324170.00151694687628349
SPI1#6688143.281729403409092.97730477982807e-050.000616468544608373
SREBF1#672045.372097078912950.006330889308531350.0275668854906694
SRF#672293.547845838843150.000685413756557910.00552728957772771
STAT1#677284.73293428507410.0002145603854675230.00246816522721033
STAT3#6774123.606673713310035.5685080397802e-050.000940594227990626
TAF1#6872232.196858987775481.29925443182519e-050.000318005234603683
TAL1#688654.266945239634310.005900858452689820.026470224033179
TBP#6908242.541785614008953.43866493745711e-071.70123508954563e-05
TCF12#6938113.342260397830020.0002479577527790030.00267553050340803
TCF7L2#693482.461754643002820.01321326614011370.0467520514417907
TFAP2C#702282.470680825110910.0129448915192520.0465291686873334
ZBTB7A#51341163.360872826457554.17459493105694e-060.000132399186153858



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C325&oldid=3067442"