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Coexpression cluster:C2530: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2530_Retinal_Mallassezderived_Bronchial_Keratinocyte_small_Hep2_Tracheal
|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$GO:0009888!tissue development!0.049679821594233!50814
|gostat_on_coexpression_clusters=GO:0006695!cholesterol biosynthetic process!2.35846206673679e-08!2224;2222;50814$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

Revision as of 15:16, 12 September 2012


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 cell1.71e-22679
eukaryotic cell1.71e-22679
embryonic cell1.39e-19248
somatic cell2.31e-17591
epithelial cell1.77e-16254
native cell1.00e-12722
mesodermal cell3.03e-11119
non-terminally differentiated cell1.44e-10180
contractile cell5.85e-0959
electrically responsive cell1.22e-0760
electrically active cell1.22e-0760
muscle cell1.88e-0754
muscle precursor cell2.19e-0757
myoblast2.19e-0757
multi-potent skeletal muscle stem cell2.19e-0757
Uber Anatomy
Ontology termp-valuen
cell layer3.51e-16312
epithelium2.21e-15309
trunk mesenchyme3.28e-15143
trunk4.02e-12216
organism subdivision4.78e-12365
multi-tissue structure7.77e-11347
anatomical cluster2.62e-10286
unilaminar epithelium3.03e-10138
epithelial tube4.21e-10118
somite6.33e-1083
paraxial mesoderm6.33e-1083
presomitic mesoderm6.33e-1083
presumptive segmental plate6.33e-1083
trunk paraxial mesoderm6.33e-1083
presumptive paraxial mesoderm6.33e-1083
mesenchyme7.07e-10238
entire embryonic mesenchyme7.07e-10238
multilaminar epithelium1.25e-0982
vasculature5.26e-0879
vascular system5.26e-0879
ectodermal placode5.31e-0829
dermomyotome6.39e-0870
larynx1.34e-079
subdivision of trunk2.53e-07113
organ part2.92e-07219


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
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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