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Coexpression cluster:C2241: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160666576584202!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192006712758724!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378455463122462!MAFF#23764;2:28.1576782449726:0.00184687618036715:0.0109234285537074!MAFK#7975;2:13.550366568915:0.0077720281209805:0.0319505154468444!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466032255777458!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284823334704586!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767059508929248!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119598129542845!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428260857943922!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172633041874579!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180824615287128!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601404734087057!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765558293215956!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404964582919868!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122961750421237!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032150412841479!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243699181689251!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229785027946457!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106674528404779!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000620137047136461!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248179730930929
|tf_chipseq_enrich=ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160666576584202!ETS1#2113;3:7.29657069165175:0.0040085737751139:0.0192006712758724!GABPB1#2553;3:5.30076287713663:0.0101267882423427:0.0378455463122462!MAFF#23764;2:28.1576782449726:0.00184687618036715:0.0109234285537074!MAFK#7975;2:13.550366568915:0.0077720281209805:0.0319505154468444!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466032255777458!NANOG#79923;2:14.6223892405063:0.00669875771536376:0.0284823334704586!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00767059508929248!NRF1#4899;3:9.15770958578318:0.00206195379173342:0.0119598129542845!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428260857943922!RAD21#5885;3:7.76627542159225:0.003341119385872:0.0172633041874579!SETDB1#9869;2:20.1600130890052:0.0035690868540764:0.0180824615287128!SIX5#147912;3:12.8150365165942:0.000766447113693038:0.00601404734087057!SMC3#9126;3:11.2836996336996:0.00111580236686805:0.00765558293215956!STAT1#6772;3:15.5299406228994:0.00043408865517555:0.00404964582919868!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122961750421237!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032150412841479!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243699181689251!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000229785027946457!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0106674528404779!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000620137047136461!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00248179730930929
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}}
}}

Revision as of 15:23, 26 November 2012


Full id: C2241_cerebellum_spinal_thalamus_medulla_substantia_occipital_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:75784669..75784698,-p1@CAPS2
Hg19::chr19:44455368..44455396,+p1@ZNF221
Hg19::chr1:144932014..144932132,-p3@PDE4DIP
Hg19::chr9:95640300..95640345,-p1@ZNF484


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism6.62e-37114
nervous system7.04e-3289
central nervous system1.28e-3181
neural tube2.66e-2956
neural rod2.66e-2956
future spinal cord2.66e-2956
neural keel2.66e-2956
regional part of nervous system2.24e-2753
regional part of brain2.24e-2753
brain3.34e-2668
future brain3.34e-2668
regional part of forebrain3.95e-2541
forebrain3.95e-2541
anterior neural tube3.95e-2541
future forebrain3.95e-2541
ectoderm-derived structure2.03e-22171
ectoderm2.03e-22171
presumptive ectoderm2.03e-22171
neural plate4.70e-2282
presumptive neural plate4.70e-2282
neurectoderm2.51e-2186
brain grey matter9.40e-2134
gray matter9.40e-2134
telencephalon1.07e-2034
regional part of telencephalon1.74e-1932
cerebral hemisphere2.00e-1932
organ system subdivision1.50e-17223
pre-chordal neural plate1.48e-1661
ecto-epithelium2.94e-16104
structure with developmental contribution from neural crest1.95e-15132
cerebral cortex3.05e-1525
pallium3.05e-1525
regional part of cerebral cortex2.53e-1422
neocortex3.87e-1320
anatomical cluster4.74e-07373
basal ganglion5.40e-079
nuclear complex of neuraxis5.40e-079
aggregate regional part of brain5.40e-079
collection of basal ganglia5.40e-079
cerebral subcortex5.40e-079
neural nucleus5.47e-079
nucleus of brain5.47e-079


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
ELF1#199744.258097958807540.003041525565781240.0160666576584202
ETS1#211337.296570691651750.00400857377511390.0192006712758724
GABPB1#255335.300762877136630.01012678824234270.0378455463122462
MAFF#23764228.15767824497260.001846876180367150.0109234285537074
MAFK#7975213.5503665689150.00777202812098050.0319505154468444
MAX#414934.839416631755340.01315737137836840.0466032255777458
NANOG#79923214.62238924050630.006698757715363760.0284823334704586
NFKB1#479045.488063424193840.001102199566301980.00767059508929248
NRF1#489939.157709585783180.002061953791733420.0119598129542845
PBX3#5090210.95725634337210.01174530180688030.0428260857943922
RAD21#588537.766275421592250.0033411193858720.0172633041874579
SETDB1#9869220.16001308900520.00356908685407640.0180824615287128
SIX5#147912312.81503651659420.0007664471136930380.00601404734087057
SMC3#9126311.28369963369960.001115802366868050.00765558293215956
STAT1#6772315.52994062289940.000434088655175550.00404964582919868
STAT3#6774410.51946499715428.16377768286615e-050.00122961750421237
TAF1#687243.343046285745290.008005664898701650.032150412841479
TBP#690843.706770687096390.005296377814784350.0243699181689251
TRIM28#10155418.59052504526258.36730015875654e-060.000229785027946457
YY1#752844.911170749853860.00171871838055440.0106674528404779
ZNF143#7702413.50087655222793.00867915035614e-050.000620137047136461
ZNF263#1012748.221841637010680.0002187871180958320.00248179730930929



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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