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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C325_Mast_Eosinophils_CD14_immature_Basophils_granulocyte_Natural
|full_id=C325_Mast_Eosinophils_CD14_immature_Basophils_granulocyte_Natural
|id=C325
|id=C325

Revision as of 16:08, 12 September 2012


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
leukocyte6.17e-33140
myeloid leukocyte6.06e-2976
CD14-positive, CD16-negative classical monocyte5.75e-2642
granulocyte monocyte progenitor cell1.77e-2571
classical monocyte2.50e-2545
hematopoietic lineage restricted progenitor cell5.57e-25124
nongranular leukocyte7.92e-25119
macrophage dendritic cell progenitor4.49e-2365
hematopoietic stem cell4.83e-22172
angioblastic mesenchymal cell4.83e-22172
monopoietic cell5.57e-2263
monocyte5.57e-2263
monoblast5.57e-2263
promonocyte5.57e-2263
myeloid lineage restricted progenitor cell1.21e-2170
hematopoietic cell5.67e-21182
hematopoietic oligopotent progenitor cell4.65e-20165
hematopoietic multipotent progenitor cell4.65e-20165
myeloid cell3.97e-16112
common myeloid progenitor3.97e-16112
connective tissue cell1.68e-09365
mesenchymal cell2.05e-09358
intermediate monocyte9.05e-079
CD14-positive, CD16-positive monocyte9.05e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.46e-27102
blood island1.46e-27102
hemolymphoid system1.14e-24112
bone marrow2.67e-2480
bone element1.38e-2186
skeletal element1.20e-16101
skeletal system1.20e-16101
lateral plate mesoderm4.00e-16216
immune system2.57e-13115
connective tissue1.24e-08375


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)

{{{tfbs_overrepresentation_jaspar}}}



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.

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