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Coexpression cluster:C1743: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0008270!zinc ion binding!0.00757246536841732!84851;376940;49855;54816$GO:0046914!transition metal ion binding!0.00757246536841732!84851;376940;49855;54816$GO:0043169!cation binding!0.0123098686752955!84851;376940;49855;54816$GO:0046872!metal ion binding!0.0123098686752955!84851;376940;49855;54816$GO:0043167!ion binding!0.0123098686752955!84851;376940;49855;54816
|gostat_on_coexpression_clusters=GO:0008270!zinc ion binding!0.00757246536841732!84851;376940;49855;54816$GO:0046914!transition metal ion binding!0.00757246536841732!84851;376940;49855;54816$GO:0043169!cation binding!0.0123098686752955!84851;376940;49855;54816$GO:0046872!metal ion binding!0.0123098686752955!84851;376940;49855;54816$GO:0043167!ion binding!0.0123098686752955!84851;376940;49855;54816
|id=C1743
|id=C1743
|ontology_enrichment_celltype=CL:0000542!8.36e-11!53;CL:0000051!8.36e-11!53;CL:0000838!1.27e-10!52;CL:0000738!6.28e-09!140;CL:0000791!3.61e-08!18;CL:0000789!3.61e-08!18;CL:0002420!3.61e-08!18;CL:0002419!3.61e-08!18;CL:0000790!3.61e-08!18;CL:0002031!2.40e-07!124;CL:0000037!2.57e-07!172;CL:0000566!2.57e-07!172;CL:0002087!5.65e-07!119;CL:0000084!8.89e-07!25;CL:0000827!8.89e-07!25
|ontology_enrichment_celltype=CL:0002242!8.49e-11!55;CL:0000542!1.53e-10!53;CL:0000051!1.53e-10!53;CL:0000838!2.30e-10!52;CL:0000738!5.12e-09!136;CL:0000037!4.46e-08!168;CL:0000566!4.46e-08!168;CL:0000791!8.57e-08!18;CL:0000789!8.57e-08!18;CL:0002420!8.57e-08!18;CL:0002419!8.57e-08!18;CL:0000790!8.57e-08!18;CL:0002031!2.19e-07!120;CL:0002032!5.79e-07!161;CL:0000837!5.79e-07!161;CL:0002087!6.91e-07!115
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.68e-46!115;UBERON:0001049!1.05e-26!57;UBERON:0005068!1.05e-26!57;UBERON:0006241!1.05e-26!57;UBERON:0007135!1.05e-26!57;UBERON:0001017!5.24e-24!82;UBERON:0000073!8.56e-24!94;UBERON:0001016!8.56e-24!94;UBERON:0005743!5.57e-23!86;UBERON:0003080!1.33e-22!42;UBERON:0002780!2.79e-22!41;UBERON:0001890!2.79e-22!41;UBERON:0006240!2.79e-22!41;UBERON:0000955!3.76e-22!69;UBERON:0006238!3.76e-22!69;UBERON:0002616!5.28e-22!59;UBERON:0002020!4.28e-18!34;UBERON:0003528!4.28e-18!34;UBERON:0001893!6.04e-18!34;UBERON:0002791!1.66e-17!33;UBERON:0002346!1.69e-17!90;UBERON:0001869!9.19e-17!32;UBERON:0003075!1.19e-16!86;UBERON:0007284!1.19e-16!86;UBERON:0002619!3.71e-13!22;UBERON:0000956!8.51e-13!25;UBERON:0000203!8.51e-13!25;UBERON:0003056!1.86e-12!61;UBERON:0001950!4.22e-12!20;UBERON:0000153!4.80e-12!129;UBERON:0007811!4.80e-12!129;UBERON:0000924!2.71e-11!173;UBERON:0006601!2.71e-11!173;UBERON:0004121!1.36e-10!169;UBERON:0000033!2.46e-10!123;UBERON:0002308!7.45e-07!9;UBERON:0000125!7.45e-07!9;UBERON:0002420!8.00e-07!9;UBERON:0007245!8.00e-07!9;UBERON:0010009!8.00e-07!9;UBERON:0010011!8.00e-07!9;UBERON:0000454!8.00e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.65e-45!114;UBERON:0001049!8.19e-26!56;UBERON:0005068!8.19e-26!56;UBERON:0006241!8.19e-26!56;UBERON:0007135!8.19e-26!56;UBERON:0001016!1.25e-24!89;UBERON:0000073!4.20e-24!53;UBERON:0002616!4.20e-24!53;UBERON:0001017!8.16e-24!81;UBERON:0002780!8.81e-22!41;UBERON:0001890!8.81e-22!41;UBERON:0003080!8.81e-22!41;UBERON:0006240!8.81e-22!41;UBERON:0000955!8.87e-22!68;UBERON:0006238!8.87e-22!68;UBERON:0003528!1.23e-17!34;UBERON:0002020!1.23e-17!34;UBERON:0001893!1.49e-17!34;UBERON:0002791!1.55e-16!32;UBERON:0001869!2.14e-16!32;UBERON:0002346!2.23e-16!86;UBERON:0003075!9.42e-16!82;UBERON:0007284!9.42e-16!82;UBERON:0002619!4.52e-13!22;UBERON:0000956!1.69e-12!25;UBERON:0000203!1.69e-12!25;UBERON:0003056!3.01e-12!61;UBERON:0001950!5.72e-12!20;UBERON:0011216!5.74e-11!223;UBERON:0004121!1.35e-10!171;UBERON:0000924!1.35e-10!171;UBERON:0006601!1.35e-10!171;UBERON:0010371!7.71e-09!104;UBERON:0010314!8.08e-08!132
|tf_chipseq_enrich=BCLAF1#9774;3:12.9915885660731:0.000917803240254255:0.00667649596774494!CCNT2#905;5:6.33620157696263:9.78880505817628e-05:0.00139017271073004!CTCF#10664;4:4.28820509846002:0.00515201558824328:0.0239334292331883!E2F4#1874;4:10.1344482522276:0.000181820150963297:0.00220291354367237!E2F6#1876;4:4.01372458535791:0.00663211823393388:0.0282922880579128!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572923873097814!GTF2F1#2962;3:7.64379652605459:0.0042841549641205:0.0203443304823253!HMGN3#9324;4:6.54283817868047:0.0010080127776835:0.0072205656027769!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00880888267789347!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0139978347202304!MYC#4609;5:5.2222818716094:0.000257394484885061:0.00276421826292143!SETDB1#9869;2:16.1280104712042:0.0058505784665934:0.0262694997623624!SIN3A#25942;4:4.32710778145211:0.00497705285576288:0.0232416017528736!SIX5#147912;3:10.2520292132754:0.00183229106867769:0.0108488376280758!SP1#6667;4:4.55870510251272:0.0040757356578168:0.0194830536601395!SP2#6668;2:10.4614121975379:0.0135319118334714:0.0477791453387849!SRF#6722;3:8.27830695730069:0.00340484607377615:0.0173581333153913!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.013528596715915!TCF7L2#6934;4:8.61614125050988:0.000343896972598245:0.00347318981928132!YY1#7528;5:4.91117074985386:0.0003499314082136:0.0035266318964026!ZNF143#7702;4:10.8007012417823:0.000141522343086319:0.00184409881342383!ZNF263#10127;4:6.57747330960854:0.000987510323790016:0.00709121223228173
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}}
}}

Revision as of 11:38, 19 October 2012


Full id: C1743_cerebellum_pituitary_pineal_lung_parietal_occipital_CD4



Phase1 CAGE Peaks

Hg19::chr15:57025759..57025811,-p2@ZNF280D
Hg19::chr15:77197655..77197716,-p1@SCAPER
Hg19::chr18:34409075..34409100,+p1@KIAA1328
Hg19::chr2:113033164..113033219,+p1@ZC3H6
Hg19::chr5:180688105..180688162,-p1@TRIM52


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:0008270zinc ion binding0.00757246536841732
GO:0046914transition metal ion binding0.00757246536841732
GO:0043169cation binding0.0123098686752955
GO:0046872metal ion binding0.0123098686752955
GO:0043167ion binding0.0123098686752955



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>


Uber Anatomy
Ontology termp-valuen
adult organism1.65e-45114
neural tube8.19e-2656
neural rod8.19e-2656
future spinal cord8.19e-2656
neural keel8.19e-2656
nervous system1.25e-2489
regional part of nervous system4.20e-2453
regional part of brain4.20e-2453
central nervous system8.16e-2481
regional part of forebrain8.81e-2241
forebrain8.81e-2241
anterior neural tube8.81e-2241
future forebrain8.81e-2241
brain8.87e-2268
future brain8.87e-2268
brain grey matter1.23e-1734
gray matter1.23e-1734
telencephalon1.49e-1734
regional part of telencephalon1.55e-1632
cerebral hemisphere2.14e-1632
neurectoderm2.23e-1686
neural plate9.42e-1682
presumptive neural plate9.42e-1682
regional part of cerebral cortex4.52e-1322
cerebral cortex1.69e-1225
pallium1.69e-1225
pre-chordal neural plate3.01e-1261
neocortex5.72e-1220
organ system subdivision5.74e-11223
ectoderm-derived structure1.35e-10171
ectoderm1.35e-10171
presumptive ectoderm1.35e-10171
ecto-epithelium7.71e-09104
structure with developmental contribution from neural crest8.08e-08132


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
BCLAF1#9774312.99158856607310.0009178032402542550.00667649596774494
CCNT2#90556.336201576962639.78880505817628e-050.00139017271073004
CTCF#1066444.288205098460020.005152015588243280.0239334292331883
E2F4#1874410.13444825222760.0001818201509632970.00220291354367237
E2F6#187644.013724585357910.006632118233933880.0282922880579128
ELF1#199754.258097958807540.0007142416939776840.00572923873097814
GTF2F1#296237.643796526054590.00428415496412050.0203443304823253
HMGN3#932446.542838178680470.00100801277768350.0072205656027769
IRF1#365946.109731002851120.001315525264767990.00880888267789347
MAX#414945.16204440720570.002526309009485180.0139978347202304
MYC#460955.22228187160940.0002573944848850610.00276421826292143
SETDB1#9869216.12801047120420.00585057846659340.0262694997623624
SIN3A#2594244.327107781452110.004977052855762880.0232416017528736
SIX5#147912310.25202921327540.001832291068677690.0108488376280758
SP1#666744.558705102512720.00407573565781680.0194830536601395
SP2#6668210.46141219753790.01353191183347140.0477791453387849
SRF#672238.278306957300690.003404846073776150.0173581333153913
TAF1#687253.343046285745290.002394600090870310.013528596715915
TCF7L2#693448.616141250509880.0003438969725982450.00347318981928132
YY1#752854.911170749853860.00034993140821360.0035266318964026
ZNF143#7702410.80070124178230.0001415223430863190.00184409881342383
ZNF263#1012746.577473309608540.0009875103237900160.00709121223228173



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.