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

Latest revision as of 11:22, 17 September 2013


Full id: C427_Eosinophils_CD4_Peripheral_Neutrophils_Basophils_mature_Mast



Phase1 CAGE Peaks

Hg19::chr10:105880871..105880889,+p5@SFR1
Hg19::chr11:58346375..58346390,-p@chr11:58346375..58346390
-
Hg19::chr14:35342116..35342120,-p@chr14:35342116..35342120
-
Hg19::chr15:72612817..72612837,+p@chr15:72612817..72612837
+
Hg19::chr15:73075463..73075507,+p1@LOC100287559
Hg19::chr15:93426078..93426080,+p2@LOC100507217
Hg19::chr19:12902289..12902307,+p1@JUNB
Hg19::chr19:39897943..39897995,+p@chr19:39897943..39897995
+
Hg19::chr1:45273015..45273052,-p1@TCTEX1D4
Hg19::chr22:41347007..41347050,-p@chr22:41347007..41347050
-
Hg19::chr2:100106078..100106095,+p@chr2:100106078..100106095
+
Hg19::chr2:208394817..208394834,+p3@CREB1
Hg19::chr3:196229754..196229771,+p@chr3:196229754..196229771
+
Hg19::chr3:53164571..53164592,+p@chr3:53164571..53164592
+
Hg19::chr5:172199488..172199515,-p@chr5:172199488..172199515
-
Hg19::chr6:30294186..30294251,+p1@TRIM39
Hg19::chr6:36650894..36650908,+p@chr6:36650894..36650908
+
Hg19::chr7:104654038..104654052,-p1@LOC100216545
Hg19::chr7:130792940..130792965,+p@chr7:130792940..130792965
+
Hg19::chr7:140624878..140624906,+p@chr7:140624878..140624906
+
Hg19::chr9:74980291..74980312,+p@chr9:74980291..74980312
+
Hg19::chrX:15353629..15353684,-p1@PIGA
Hg19::chrX:15693462..15693479,-p@chrX:15693462..15693479
-


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:0003712transcription cofactor activity0.018187435853225
GO:0000506glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex0.018187435853225
GO:0046983protein dimerization activity0.018187435853225
GO:0017176phosphatidylinositol N-acetylglucosaminyltransferase activity0.018187435853225
GO:0008134transcription factor binding0.0196061772370119
GO:0006506GPI anchor biosynthetic process0.045457632223145
GO:0006505GPI anchor metabolic process0.045457632223145
GO:0043565sequence-specific DNA binding0.045457632223145
GO:0046489phosphoinositide biosynthetic process0.045457632223145
GO:0005515protein binding0.045457632223145
GO:0008375acetylglucosaminyltransferase activity0.045457632223145
GO:0046474glycerophospholipid biosynthetic process0.045457632223145
GO:0006497protein amino acid lipidation0.045457632223145
GO:0042158lipoprotein biosynthetic process0.045457632223145
GO:0019222regulation of metabolic process0.045457632223145



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
leukocyte8.72e-67136
hematopoietic lineage restricted progenitor cell4.17e-56120
hematopoietic stem cell9.06e-54168
angioblastic mesenchymal cell9.06e-54168
nongranular leukocyte5.69e-53115
hematopoietic cell5.40e-52177
hematopoietic oligopotent progenitor cell7.17e-50161
hematopoietic multipotent progenitor cell7.17e-50161
classical monocyte1.67e-3442
CD14-positive, CD16-negative classical monocyte1.67e-3442
myeloid leukocyte5.27e-3472
defensive cell2.55e-3048
phagocyte2.55e-3048
granulocyte monocyte progenitor cell3.03e-2967
myeloid lineage restricted progenitor cell4.77e-2866
macrophage dendritic cell progenitor7.33e-2761
monopoietic cell2.41e-2559
monocyte2.41e-2559
monoblast2.41e-2559
promonocyte2.41e-2559
nucleate cell7.10e-2555
myeloid cell1.10e-24108
common myeloid progenitor1.10e-24108
lymphoid lineage restricted progenitor cell1.12e-2452
lymphocyte6.46e-2453
common lymphoid progenitor6.46e-2453
mesenchymal cell7.04e-16354
connective tissue cell7.59e-15361
T cell4.82e-1225
pro-T cell4.82e-1225
mature alpha-beta T cell9.05e-1218
alpha-beta T cell9.05e-1218
immature T cell9.05e-1218
mature T cell9.05e-1218
immature alpha-beta T cell9.05e-1218
stuff accumulating cell1.14e-1187
lymphocyte of B lineage2.65e-1124
pro-B cell2.65e-1124
motile cell1.68e-10386
granulocyte8.07e-098
intermediate monocyte1.35e-089
CD14-positive, CD16-positive monocyte1.35e-089
B cell2.61e-0814
multi fate stem cell5.97e-08427
stem cell9.86e-08441
somatic stem cell2.08e-07433
blood cell3.50e-0711
CD8-positive, alpha-beta T cell5.89e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system6.17e-3798
blood island6.17e-3798
hemolymphoid system1.21e-32108
bone marrow1.82e-2676
immune system2.57e-2493
bone element4.58e-2482
skeletal element3.13e-2090
skeletal system2.23e-16100
connective tissue8.05e-14371
lateral plate mesoderm6.32e-11203
blood8.71e-1015
haemolymphatic fluid8.71e-1015
organism substance8.71e-1015


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)
MA0003.12.95302
MA0004.10.888963
MA0006.12.34533
MA0007.10.137043
MA0009.10.510226
MA0014.11.7581
MA0017.10.583727
MA0019.10.250001
MA0024.10.419164
MA0025.11.52543
MA0027.12.07466
MA0028.10.247069
MA0029.10.435662
MA0030.10.425859
MA0031.10.371592
MA0038.10.21714
MA0040.10.440685
MA0041.10.160207
MA0042.10.433314
MA0043.12.19569
MA0046.10.500598
MA0048.10.48811
MA0050.10.14079
MA0051.10.214141
MA0052.10.444013
MA0055.10.970573
MA0056.10
MA0057.12.41151
MA0058.11.07555
MA0059.10.642105
MA0060.11.08732
MA0061.10.625508
MA0063.10
MA0066.10.217443
MA0067.10.802392
MA0068.10.724143
MA0069.10.497197
MA0070.10.487346
MA0071.10.556315
MA0072.10.483399
MA0073.12.43243
MA0074.10.213609
MA0076.10.102323
MA0077.10.476645
MA0078.10.287843
MA0081.10.642506
MA0083.10.516887
MA0084.10.981601
MA0087.10.481255
MA0088.10.770434
MA0089.10
MA0090.10.110205
MA0091.10.15013
MA0092.10.400168
MA0093.10.856503
MA0095.10
MA0098.10
MA0100.10.227084
MA0101.11.30976
MA0103.10.214965
MA0105.10.852739
MA0106.10.247115
MA0107.10.966237
MA0108.20.965791
MA0109.10
MA0111.10.375752
MA0113.10.259368
MA0114.10.94303
MA0115.10.730438
MA0116.10.349495
MA0117.10.543727
MA0119.10.0851434
MA0122.10.567011
MA0124.10.691722
MA0125.10.614264
MA0130.10
MA0131.10.816303
MA0132.10
MA0133.10
MA0135.10.537249
MA0136.10.222179
MA0139.10.173133
MA0140.10.188358
MA0141.10.637815
MA0142.10.345512
MA0143.10.259501
MA0144.10.0312488
MA0145.11.44482
MA0146.10.21112
MA0147.10.998135
MA0148.10.164295
MA0149.10.18183
MA0062.20.362551
MA0035.20.18788
MA0039.23.28055
MA0138.20.288795
MA0002.20.221099
MA0137.20.073361
MA0104.21.08293
MA0047.20.238164
MA0112.20.588343
MA0065.20.652686
MA0150.10.70627
MA0151.10
MA0152.10.192836
MA0153.10.598889
MA0154.10.235715
MA0155.11.29059
MA0156.10.0744198
MA0157.10.323429
MA0158.10
MA0159.10.358237
MA0160.10.99551
MA0161.10
MA0162.13.07977
MA0163.13.10375
MA0164.10.268764
MA0080.20.498167
MA0018.21.98486
MA0099.20.563326
MA0079.211.2848
MA0102.21.01759
MA0258.10.0284286
MA0259.10.668401
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
BRCA1#67287.020601962860449.06157856366518e-060.000242165354045708
CCNT2#905123.305844301023985.76359523990671e-050.000960804666018542
CEBPB#1051113.81228799495973.80662840696668e-050.000718136676653166
CHD2#110673.14818086255730.004784156347452220.0224825641095915
E2F1#1869112.347012233203160.002920515161053220.0157793938388638
E2F4#187463.304711386595940.007538279829342990.0310788886426951
E2F6#1876122.617646468711680.0005776502845754520.00484922579139744
EGR1#1958132.819405575327470.0001246715999219350.00166121168974827
ELF1#1997142.591885714056760.0001385673248892810.0018094314633798
ETS1#211393.806906447818310.0002713333239755710.00289633902521307
FOS#235372.73850813748960.01022841326632460.0380822520809125
FOSL2#235553.680478392296020.00986822700574640.0370702740901067
FOXA1#316962.89080515201360.014167818768390.049706826940066
GABPB1#255392.765615414158240.002816008092142730.0154132943312874
GTF2F1#2962105.538982989894633.88727897856282e-060.000126830218444899
HEY1#23462172.986169031860741.00637621778943e-064.25009809177964e-05
IRF1#365992.988455381829350.00162532362328310.010172420081025
JUND#3727123.649389882715322.09167356596463e-050.000461453940759992
MAX#4149123.366550700351544.78984534698273e-050.000832911518803745
MXI1#4601114.764229909406624.44187487408454e-060.000139060242798116
MYC#4609153.405836003223521.72467631994131e-066.50500072872338e-05
NFKB1#4790174.056394704838928.74058419112347e-096.71712930343446e-07
NR3C1#290863.906006086392970.003322737590041340.0171853311130752
NR4A1#31641119.9396495781960.00830485696721050.0327166442909923
NRF1#489994.777935436060794.65808628481129e-050.000815020729601953
PAX5#5079102.89981110051210.0009940761806075530.00713394641836544
PBX3#509065.716829396541950.0004641954187087440.00427288078040918
POLR2A#5430232.147453176558072.31778206774654e-081.63780000929216e-06
POU2F2#5452135.146939684810991.31866051845867e-077.51744464450354e-06
RDBP#7936213.35986121652390.009780990511066760.0367769609729731
REST#597872.936965261430270.00701343320914610.0296297055511512
RFX5#599373.666755469146330.002014615479728780.0117119079369549
SIN3A#25942143.292364616322268.14655446505413e-060.000225382252126037
SMARCB1#659864.761578029867150.001212617011883510.00816218794174413
SP1#6667122.973068545116990.0001670913457759930.00204702088697935
SPI1#6688113.923806895380442.89567448032055e-050.000605811993289659
TAF1#6872182.616297093191972.3449581143056e-068.32727237334113e-05
TAF7#687983.976719793017010.0005032133903997930.00443465558011678
TBP#6908172.739787029592983.68674799878908e-060.000120778003213781
TCF12#693883.698944313803970.0008180204946780320.00623145459107797
USF1#7391102.765869250959980.001446902049559220.00927756650011763
YY1#7528142.989408282519742.60243933511817e-050.000562143043889155
ZBTB7A#5134192.876834076994920.002132449810949820.0123242170220679
ZNF263#1012793.217242379699830.0009524135052960.00685662880537734



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:C427&oldid=3067544"