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Coexpression cluster:C4168: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190462838909367!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661527632498795!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130013253135498!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326229131568773!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463434599735605!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763663659457695!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899262556536842!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154445214741944!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128372284434879!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253742148156335!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000738703434729602!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.0019996127267354!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246271235108961!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136905682974081!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277439807466035!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247060261164471!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000941396902933208
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0190462838909367!CHD2#1106;3:10.3440228341169:0.000903370110274688:0.00661527632498795!CTBP2#1488;3:62.7170003393281:4.049570681927e-06:0.000130013253135498!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326229131568773!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0463434599735605!ETS1#2113;3:9.72876092220234:0.00108584009258484:0.00763663659457695!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899262556536842!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154445214741944!IRF1#3659;3:7.6371637535639:0.00224469274729724:0.0128372284434879!IRF3#3661;3:46.9819522114896:9.63568551583244e-06:0.000253742148156335!NANOG#79923;3:29.2447784810127:3.99627955670032e-05:0.000738703434729602!NFYA#4800;3:18.4255806998305:0.000159813550781416:0.0019996127267354!NFYB#4801;3:16.7597932535365:0.000212364992329618:0.00246271235108961!PBX3#5090;3:21.9145126867441:9.49854535978121e-05:0.00136905682974081!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0277439807466035!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247060261164471!SP2#6668;3:26.1535304938446:5.58768218891694e-05:0.000941396902933208
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}}
}}

Revision as of 16:35, 26 November 2012


Full id: C4168_optic_substantia_spinal_left_pineal_globus_thalamus



Phase1 CAGE Peaks

Hg19::chr2:198669308..198669328,+p1@PLCL1
Hg19::chr2:198669338..198669358,+p2@PLCL1
Hg19::chr2:198669365..198669376,+p3@PLCL1


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
leukocyte1.65e-08136
mature alpha-beta T cell4.33e-0718
alpha-beta T cell4.33e-0718
immature T cell4.33e-0718
mature T cell4.33e-0718
immature alpha-beta T cell4.33e-0718
myeloid leukocyte8.22e-0772
Uber Anatomy
Ontology termp-valuen
adult organism1.46e-44114
neural tube8.32e-2656
neural rod8.32e-2656
future spinal cord8.32e-2656
neural keel8.32e-2656
regional part of nervous system5.88e-2453
regional part of brain5.88e-2453
regional part of forebrain4.96e-2141
forebrain4.96e-2141
anterior neural tube4.96e-2141
future forebrain4.96e-2141
central nervous system6.47e-2081
brain1.56e-1868
future brain1.56e-1868
brain grey matter1.28e-1734
gray matter1.28e-1734
telencephalon1.69e-1734
nervous system1.80e-1789
neural plate1.96e-1682
presumptive neural plate1.96e-1682
regional part of telencephalon2.24e-1632
cerebral hemisphere3.19e-1632
neurectoderm1.85e-1486
regional part of cerebral cortex9.73e-1422
neocortex9.07e-1320
cerebral cortex1.55e-1225
pallium1.55e-1225
pre-chordal neural plate2.17e-1161
structure with developmental contribution from neural crest4.27e-11132
ecto-epithelium5.78e-09104
lateral plate mesoderm1.24e-08203
tube3.09e-08192
hematopoietic system1.57e-0798
blood island1.57e-0798
hemolymphoid system7.78e-07108


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
CCNT2#90536.336201576962630.003930750035764890.0190462838909367
CHD2#1106310.34402283411690.0009033701102746880.00661527632498795
CTBP2#1488362.71700033932814.049570681927e-060.000130013253135498
E2F1#186934.907389214879320.008460985347239390.0326229131568773
ELF1#199734.258097958807540.01295179875054610.0463434599735605
ETS1#211339.728760922202340.001085840092584840.00763663659457695
FOS#235338.99795530889440.001372499272417130.00899262556536842
GABPB1#255337.067683836182170.002832212825417420.0154445214741944
IRF1#365937.63716375356390.002244692747297240.0128372284434879
IRF3#3661346.98195221148969.63568551583244e-060.000253742148156335
NANOG#79923329.24477848101273.99627955670032e-050.000738703434729602
NFYA#4800318.42558069983050.0001598135507814160.0019996127267354
NFYB#4801316.75979325353650.0002123649923296180.00246271235108961
PBX3#5090321.91451268674419.49854535978121e-050.00136905682974081
SIN3A#2594235.408884726815140.006318961977991520.0277439807466035
SP1#666735.69838137814090.005403962701712170.0247060261164471
SP2#6668326.15353049384465.58768218891694e-050.000941396902933208



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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