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{{Coexpression_clusters
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biosynthetic process!2.35846206673679e-08!2224;2222;50814$GO:0016126!sterol biosynthetic process!2.7973410948078e-08!2224;2222;50814$GO:0008203!cholesterol metabolic process!2.60032406071113e-07!2224;2222;50814$GO:0006694!steroid biosynthetic process!2.7490233849884e-07!2224;2222;50814$GO:0016125!sterol metabolic process!2.7490233849884e-07!2224;2222;50814$GO:0008202!steroid metabolic process!3.11636752412651e-06!2224;2222;50814$GO:0008610!lipid biosynthetic process!8.93433186074538e-06!2224;2222;50814$GO:0004659!prenyltransferase activity!9.14037355238191e-06!2224;2222$GO:0006066!alcohol metabolic process!1.66208797318529e-05!2224;2222;50814$GO:0008299!isoprenoid biosynthetic process!1.95292984653651e-05!2224;2222$GO:0006720!isoprenoid metabolic process!3.13236575847922e-05!2224;2222$GO:0044255!cellular lipid metabolic process!6.42619524810821e-05!2224;2222;50814$GO:0016765!transferase activity, transferring alkyl or aryl (other than methyl) groups!9.10383300825682e-05!2224;2222$GO:0006629!lipid metabolic process!0.000103018853577011!2224;2222;50814$GO:0004310!farnesyl-diphosphate farnesyltransferase activity!0.000369789826916284!2222$GO:0047012!sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity!0.000369789826916284!50814$GO:0004337!geranyltranstransferase activity!0.000657384784818225!2224$GO:0004161!dimethylallyltranstransferase activity!0.000657384784818225!2224$GO:0004311!farnesyltranstransferase activity!0.00124549783979476!2222$GO:0009058!biosynthetic process!0.00126128254597198!2224;2222;50814$GO:0003854!3-beta-hydroxy-delta5-steroid dehydrogenase activity!0.00309827870602796!50814$GO:0022404!molting cycle process!0.00409408397409858!50814$GO:0001942!hair follicle development!0.00409408397409858!50814$GO:0042633!hair cycle!0.00409408397409858!50814$GO:0042303!molting cycle!0.00409408397409858!50814$GO:0022405!hair cycle process!0.00409408397409858!50814$GO:0005783!endoplasmic reticulum!0.00519523953746089!2222;50814$GO:0016229!steroid dehydrogenase activity!0.0067557024387043!50814$GO:0016491!oxidoreductase activity!0.0140882656807064!2222;50814$GO:0005737!cytoplasm!0.0238510504393937!2224;2222;50814$GO:0008544!epidermis development!0.0256644984393836!50814$GO:0007398!ectoderm development!0.0268795976235625!50814$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0274868037710153!50814$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0285746974756521!50814$GO:0016740!transferase activity!0.049679821594233!2224;2222$GO:0009888!tissue 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194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.00636811,MA0074.1;1.91637,MA0076.1;1.51122,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.536981,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;1.33363,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;1.83481,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.569905,MA0146.1;0.8309,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;1.83323,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;1.75253,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;1.78721,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.0626799,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2530_Retinal_Mallassezderived_Bronchial_Keratinocyte_small_Hep2_Tracheal
|gostat_on_coexpression_clusters=GO:0006695!cholesterol biosynthetic process!2.35846206673679e-08!2224;2222;50814$GO:0016126!sterol biosynthetic process!2.7973410948078e-08!2224;2222;50814$GO:0008203!cholesterol metabolic process!2.60032406071113e-07!2224;2222;50814$GO:0006694!steroid biosynthetic process!2.7490233849884e-07!2224;2222;50814$GO:0016125!sterol metabolic process!2.7490233849884e-07!2224;2222;50814$GO:0008202!steroid metabolic process!3.11636752412651e-06!2224;2222;50814$GO:0008610!lipid biosynthetic process!8.93433186074538e-06!2224;2222;50814$GO:0004659!prenyltransferase activity!9.14037355238191e-06!2224;2222$GO:0006066!alcohol metabolic process!1.66208797318529e-05!2224;2222;50814$GO:0008299!isoprenoid biosynthetic process!1.95292984653651e-05!2224;2222$GO:0006720!isoprenoid metabolic process!3.13236575847922e-05!2224;2222$GO:0044255!cellular lipid metabolic process!6.42619524810821e-05!2224;2222;50814$GO:0016765!transferase activity, transferring alkyl or aryl (other than methyl) groups!9.10383300825682e-05!2224;2222$GO:0006629!lipid metabolic process!0.000103018853577011!2224;2222;50814$GO:0004310!farnesyl-diphosphate farnesyltransferase activity!0.000369789826916284!2222$GO:0047012!sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity!0.000369789826916284!50814$GO:0004337!geranyltranstransferase activity!0.000657384784818225!2224$GO:0004161!dimethylallyltranstransferase activity!0.000657384784818225!2224$GO:0004311!farnesyltranstransferase activity!0.00124549783979476!2222$GO:0009058!biosynthetic process!0.00126128254597198!2224;2222;50814$GO:0003854!3-beta-hydroxy-delta5-steroid dehydrogenase activity!0.00309827870602796!50814$GO:0022404!molting cycle process!0.00409408397409858!50814$GO:0001942!hair follicle development!0.00409408397409858!50814$GO:0042633!hair cycle!0.00409408397409858!50814$GO:0042303!molting cycle!0.00409408397409858!50814$GO:0022405!hair cycle process!0.00409408397409858!50814$GO:0005783!endoplasmic reticulum!0.00519523953746089!2222;50814$GO:0016229!steroid dehydrogenase activity!0.0067557024387043!50814$GO:0016491!oxidoreductase activity!0.0140882656807064!2222;50814$GO:0005737!cytoplasm!0.0238510504393937!2224;2222;50814$GO:0008544!epidermis development!0.0256644984393836!50814$GO:0007398!ectoderm development!0.0268795976235625!50814$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0274868037710153!50814$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0285746974756521!50814$GO:0016740!transferase activity!0.049679821594233!2224;2222$GO:0009888!tissue development!0.049679821594233!50814
|id=C2530
}}

Latest revision as of 12:07, 17 September 2013


Full id: C2530_Retinal_Mallassezderived_Bronchial_Keratinocyte_small_Hep2_Tracheal



Phase1 CAGE Peaks

Hg19::chr1:155278605..155278621,+p2@FDPS
Hg19::chr1:155278625..155278745,+p1@FDPS
Hg19::chr8:11660227..11660306,+p1@FDFT1
Hg19::chrX:151999599..151999615,+p1@NSDHL


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
1.25863435561633e-060.000265571849035045219Steroid biosynthesis (KEGG):00100
6.31961929821581e-050.010000797539426531138Metabolic pathways (KEGG):01100
1.17374162251993e-107.42978447055117e-08315Cholesterol Biosynthesis (Wikipathways):WP1795
1.02702753121762e-060.0002655718490350453289Metabolism of lipids and lipoproteins (Reactome):REACT_22258



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:0006695cholesterol biosynthetic process2.35846206673679e-08
GO:0016126sterol biosynthetic process2.7973410948078e-08
GO:0008203cholesterol metabolic process2.60032406071113e-07
GO:0006694steroid biosynthetic process2.7490233849884e-07
GO:0016125sterol metabolic process2.7490233849884e-07
GO:0008202steroid metabolic process3.11636752412651e-06
GO:0008610lipid biosynthetic process8.93433186074538e-06
GO:0004659prenyltransferase activity9.14037355238191e-06
GO:0006066alcohol metabolic process1.66208797318529e-05
GO:0008299isoprenoid biosynthetic process1.95292984653651e-05
GO:0006720isoprenoid metabolic process3.13236575847922e-05
GO:0044255cellular lipid metabolic process6.42619524810821e-05
GO:0016765transferase activity, transferring alkyl or aryl (other than methyl) groups9.10383300825682e-05
GO:0006629lipid metabolic process0.000103018853577011
GO:0004310farnesyl-diphosphate farnesyltransferase activity0.000369789826916284
GO:0047012sterol-4-alpha-carboxylate 3-dehydrogenase (decarboxylating) activity0.000369789826916284
GO:0004337geranyltranstransferase activity0.000657384784818225
GO:0004161dimethylallyltranstransferase activity0.000657384784818225
GO:0004311farnesyltranstransferase activity0.00124549783979476
GO:0009058biosynthetic process0.00126128254597198
GO:00038543-beta-hydroxy-delta5-steroid dehydrogenase activity0.00309827870602796
GO:0022404molting cycle process0.00409408397409858
GO:0001942hair follicle development0.00409408397409858
GO:0042633hair cycle0.00409408397409858
GO:0042303molting cycle0.00409408397409858
GO:0022405hair cycle process0.00409408397409858
GO:0005783endoplasmic reticulum0.00519523953746089
GO:0016229steroid dehydrogenase activity0.0067557024387043
GO:0016491oxidoreductase activity0.0140882656807064
GO:0005737cytoplasm0.0238510504393937
GO:0008544epidermis development0.0256644984393836
GO:0007398ectoderm development0.0268795976235625
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0274868037710153
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0285746974756521
GO:0016740transferase activity0.049679821594233
GO:0009888tissue development0.049679821594233



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
animal cell5.00e-23679
eukaryotic cell5.00e-23679
embryonic cell4.11e-19250
somatic cell1.47e-17588
epithelial cell1.01e-14253
native cell2.42e-14722
mesodermal cell1.32e-11121
contractile cell6.89e-0959
electrically responsive cell8.04e-0861
electrically active cell8.04e-0861
muscle precursor cell9.97e-0858
myoblast9.97e-0858
multi-potent skeletal muscle stem cell9.97e-0858
muscle cell1.03e-0755
non-terminally differentiated cell3.53e-07106
ectodermal cell7.43e-0772
Uber Anatomy
Ontology termp-valuen
cell layer7.93e-16309
epithelium5.58e-15306
organism subdivision9.81e-13264
unilaminar epithelium3.25e-12148
multi-tissue structure7.25e-11342
anatomical cluster2.57e-10373
multilaminar epithelium4.39e-1083
trunk mesenchyme5.91e-10122
epithelial vesicle7.91e-1078
mesenchyme2.46e-09160
entire embryonic mesenchyme2.46e-09160
trunk5.61e-09199
epithelial tube6.46e-09117
ectodermal placode1.15e-0831
somite1.99e-0871
presomitic mesoderm1.99e-0871
presumptive segmental plate1.99e-0871
dermomyotome1.99e-0871
trunk paraxial mesoderm1.99e-0871
vasculature2.09e-0878
vascular system2.09e-0878
paraxial mesoderm2.64e-0872
presumptive paraxial mesoderm2.64e-0872
dense mesenchyme tissue5.94e-0873
larynx1.23e-079
primordium1.97e-07160
organ part5.51e-07218


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)
MA0003.10.443649
MA0004.10.71247
MA0006.11.31813
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.19.62028
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.00636811
MA0074.11.91637
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.11.33363
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.11.83481
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.21.83323
MA0039.20.483275
MA0138.20.928035
MA0002.21.75253
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#467211.23158726300440.01119559039922220.0411289973514498
BRCA1#672315.13817298241780.0004682184421431190.00430195002014474
CCNT2#90546.336201576962630.0006203100587215640.00512292916517646
CEBPB#105135.978360719368610.007153832484726970.0297297803856751
CHD2#1106410.34402283411698.73193255208051e-050.00129098853879776
ELF1#199744.258097958807540.003041525565781240.016094334932595
EP300#203335.08045629466740.01144298405398240.0418963649996097
ESR1#2099215.38430164807720.006065572629693510.0268401974354953
ETS1#211349.728760922202340.0001115955317418140.00154595115261749
FOS#235348.99795530889440.0001525147711168630.00194939299726766
FOSL2#2355416.93020060456171.2165416097647e-050.000304030603451102
GATA1#2623310.17023110785030.001515158168498270.00966419958225181
GATA2#262439.55869880016550.001818151618357440.0109004556182338
GATA3#2625213.6182581786030.00769665208093340.0316930428845406
GTF2F1#296239.554745657568240.001820362319304780.010899943829026
HEY1#2346244.040111043105710.00375304636917980.0186153310101999
HMGN3#932436.133910792512940.006640696683324720.0282976751768636
IRF1#365947.63716375356390.0002938853996185490.00307607709468447
IRF3#3661335.23646415861723.79279212646878e-050.000719817221327045
MAX#414934.839416631755340.01315737137836840.0466253633749122
MXI1#460149.96157162875930.0001015224754950450.00142416464986259
NFYA#4800418.42558069983058.67100748407158e-060.000234426961074023
NFYB#4801416.75979325353651.26678572070404e-050.00031137169659828
NR2C2#7182216.30730545262040.005411825344648220.0245570745207558
PBX3#5090210.95725634337210.01174530180688030.0428455317991189
REST#597837.237521537096020.004104697304192610.0195802723007478
RFX5#5993412.04791082719514.74457429336527e-050.000826966946970586
SIN3A#2594245.408884726815140.001168172384885160.00796674648720261
SP1#666745.69838137814090.0009482606065333980.00684513336229897
SP2#6668213.07676524692230.008330036536614940.0328096502431561
SREBF1#6720447.00584944048832.04523668136926e-071.10331856283845e-05
SREBF2#67214436.9432624113482.70480926640298e-113.17758801995344e-09
STAT1#6772210.35329374859960.01310777476171260.0464922020152319
TAF1#687243.343046285745290.008005664898701650.0322371852388765
TAF7#687938.574802053692940.00250055433515240.014034576215014
TAL1#6886214.93430833872010.006428077577888070.0279481284774594
TBP#690843.706770687096390.005296377814784350.0244334291531544
TCF7L2#693438.077632422353010.002978381685834620.0158647016314011
THAP1#55145215.68457230142570.005840469678357920.0262489376339626
USF1#739134.771124457905970.01370465887188020.048305800469804
USF2#739239.74414803880220.001718341848410070.0107205438653584
ZBTB33#10009323.74854377248590.0001229451908818380.0016555276934642
ZNF143#7702310.12565741417090.001534861610688180.00976839803526285



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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