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Coexpression cluster:C1129: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;5:3.82875455219645:0.00338737119268134:0.0172901451538266!CTCFL#140690;4:11.2836996336996:0.000203273626505993:0.00241328797074677!E2F1#1869;5:3.50527801062809:0.00509055358791505:0.0236847830965501!E2F6#1876;5:3.58368266549813:0.00459810189782724:0.0217225839827737!EGR1#1958;6:4.27558208126583:0.000376213061986645:0.00373562616284686!HDAC2#3066;4:7.66606870664358:0.000898637344705782:0.0066856237101957!RAD21#5885;5:7.3964527824688:0.000149101450522837:0.00192294472600081!SMARCB1#6598;4:10.4301233035185:0.000275586383300937:0.00293603654856336!TCF7L2#6934;4:6.15438660750705:0.00206467614813804:0.0119696204404878!TFAP2A#7020;3:7.07941473130498:0.00645255447218097:0.028027713214112!TFAP2C#7022;4:6.17670206277727:0.00203675492806902:0.0118274477582764!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00603000311869647
|tf_chipseq_enrich=CTCF#10664;5:3.82875455219645:0.00338737119268134:0.0172901451538266!CTCFL#140690;4:11.2836996336996:0.000203273626505993:0.00241328797074677!E2F1#1869;5:3.50527801062809:0.00509055358791505:0.0236847830965501!E2F6#1876;5:3.58368266549813:0.00459810189782724:0.0217225839827737!EGR1#1958;6:4.27558208126583:0.000376213061986645:0.00373562616284686!HDAC2#3066;4:7.66606870664358:0.000898637344705782:0.0066856237101957!RAD21#5885;5:7.3964527824688:0.000149101450522837:0.00192294472600081!SMARCB1#6598;4:10.4301233035185:0.000275586383300937:0.00293603654856336!TCF7L2#6934;4:6.15438660750705:0.00206467614813804:0.0119696204404878!TFAP2A#7020;3:7.07941473130498:0.00645255447218097:0.028027713214112!TFAP2C#7022;4:6.17670206277727:0.00203675492806902:0.0118274477582764!ZBTB7A#51341;5:5.25136379133993:0.000768769248321446:0.00603000311869647
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}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1129_mature_hippocampus_spinal_substantia_corpus_thalamus_breast



Phase1 CAGE Peaks

Hg19::chr11:111782696..111782707,-p3@CRYAB
Hg19::chr3:138067105..138067137,+p6@MRAS
Hg19::chr3:138067461..138067488,+p3@MRAS
Hg19::chr3:138067492..138067519,+p2@MRAS
Hg19::chr3:138067521..138067553,+p5@MRAS
Hg19::chr4:2061045..2061064,+p1@NAT8L
Hg19::chr6:24495348..24495380,-p5@GPLD1


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:0004621glycosylphosphatidylinositol phospholipase D activity0.0127157931504338
GO:0032387negative regulation of intracellular transport0.0127157931504338
GO:0004630phospholipase D activity0.0254270947850913
GO:0030742GTP-dependent protein binding0.0349545369002825



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
fat cell1.57e-0915
Uber Anatomy
Ontology termp-valuen
adult organism1.05e-28114
neural tube5.61e-2656
neural rod5.61e-2656
future spinal cord5.61e-2656
neural keel5.61e-2656
structure with developmental contribution from neural crest1.64e-24132
regional part of nervous system3.91e-2453
regional part of brain3.91e-2453
neural plate4.33e-2282
presumptive neural plate4.33e-2282
central nervous system6.29e-2281
brain5.27e-2168
future brain5.27e-2168
regional part of forebrain3.40e-1941
forebrain3.40e-1941
anterior neural tube3.40e-1941
future forebrain3.40e-1941
nervous system8.45e-1989
multi-cellular organism9.00e-19656
neurectoderm9.30e-1986
anatomical system3.43e-18624
anatomical group7.67e-18625
multi-tissue structure9.89e-18342
organ1.81e-17503
brain grey matter4.11e-1734
gray matter4.11e-1734
telencephalon7.37e-1734
ecto-epithelium3.06e-16104
regional part of telencephalon8.28e-1632
cerebral hemisphere9.53e-1632
pre-chordal neural plate6.66e-1561
developing anatomical structure4.30e-13581
ectoderm-derived structure5.02e-13171
ectoderm5.02e-13171
presumptive ectoderm5.02e-13171
regional part of cerebral cortex1.16e-1222
cerebral cortex6.45e-1225
pallium6.45e-1225
embryonic structure7.38e-12564
embryo8.98e-12592
germ layer9.19e-12560
germ layer / neural crest9.19e-12560
embryonic tissue9.19e-12560
presumptive structure9.19e-12560
germ layer / neural crest derived structure9.19e-12560
epiblast (generic)9.19e-12560
neocortex2.20e-1120
anatomical cluster5.20e-11373
epithelium7.51e-11306
cell layer1.29e-10309
tube4.71e-10192
anatomical conduit1.00e-09240
organ system subdivision2.97e-09223
tissue1.97e-08773
organ part2.51e-08218
posterior neural tube5.85e-0815
chordal neural plate5.85e-0815
neural nucleus8.62e-079
nucleus of brain8.62e-079
basal ganglion9.38e-079
nuclear complex of neuraxis9.38e-079
aggregate regional part of brain9.38e-079
collection of basal ganglia9.38e-079
cerebral subcortex9.38e-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
CTCF#1066453.828754552196450.003387371192681340.0172901451538266
CTCFL#140690411.28369963369960.0002032736265059930.00241328797074677
E2F1#186953.505278010628090.005090553587915050.0236847830965501
E2F6#187653.583682665498130.004598101897827240.0217225839827737
EGR1#195864.275582081265830.0003762130619866450.00373562616284686
HDAC2#306647.666068706643580.0008986373447057820.0066856237101957
RAD21#588557.39645278246880.0001491014505228370.00192294472600081
SMARCB1#6598410.43012330351850.0002755863833009370.00293603654856336
TCF7L2#693446.154386607507050.002064676148138040.0119696204404878
TFAP2A#702037.079414731304980.006452554472180970.028027713214112
TFAP2C#702246.176702062777270.002036754928069020.0118274477582764
ZBTB7A#5134155.251363791339930.0007687692483214460.00603000311869647



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.