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Coexpression cluster:C334

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Full id: C334_cerebellum_pineal_occipital_pituitary_amygdala_medial_caudate



Phase1 CAGE Peaks

Hg19::chr10:101190668..101190736,+p1@ENST00000416191
Hg19::chr11:17230061..17230092,+p@chr11:17230061..17230092
+
Hg19::chr11:57417405..57417423,-p2@YPEL4
Hg19::chr12:118406777..118406811,-p1@KSR2
Hg19::chr12:79258463..79258477,+p10@SYT1
Hg19::chr12:9066766..9066866,+p1@PHC1
Hg19::chr13:25542609..25542639,-p1@TPTE2P1
Hg19::chr13:29394076..29394108,+p@chr13:29394076..29394108
+
Hg19::chr14:100070869..100070889,+p1@ENST00000502101
Hg19::chr14:103524166..103524207,+p1@AK057714
Hg19::chr14:58797974..58798011,+p3@ARID4A
Hg19::chr14:66975213..66975239,+p2@GPHN
Hg19::chr14:94024982..94024986,+p@chr14:94024982..94024986
+
Hg19::chr15:61521462..61521482,-p4@RORA
Hg19::chr15:65204075..65204119,+p1@ANKDD1A
Hg19::chr17:50235645..50235676,-p2@CA10
Hg19::chr18:29265423..29265443,-p@chr18:29265423..29265443
-
Hg19::chr19:28284917..28284960,+p1@AK095009
Hg19::chr19:44406012..44406044,+p@chr19:44406012..44406044
+
Hg19::chr1:147719007..147719042,-p@chr1:147719007..147719042
-
Hg19::chr1:197237324..197237332,+p5@CRB1
Hg19::chr20:5892037..5892067,+p2@CHGB
Hg19::chr21:17442799..17442832,+p17@LINC00478
Hg19::chr21:17443471..17443515,+p10@LINC00478
Hg19::chr22:20850171..20850221,+p3@MED15
Hg19::chr4:176987131..176987162,+p2@WDR17
Hg19::chr4:176987163..176987196,+p3@WDR17
Hg19::chr4:57276661..57276679,+p1@ENST00000416157
Hg19::chr5:139487724..139487763,+p@chr5:139487724..139487763
+
Hg19::chr5:161494464..161494499,+p4@GABRG2
Hg19::chr6:46620738..46620755,+p2@SLC25A27
Hg19::chr6:80247381..80247389,+p@chr6:80247381..80247389
+
Hg19::chrX:46988715..46988759,+p@chrX:46988715..46988759
+
Hg19::chrX:83443478..83443513,-p@chrX:83443478..83443513
-


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
6.75939345257143e-050.0427869605547771222{DNM1,22} (Static Module):NA



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 organism1.15e-43115
regional part of nervous system1.69e-3894
nervous system1.69e-3894
central nervous system4.92e-3782
neural tube4.64e-3357
neural rod4.64e-3357
future spinal cord4.64e-3357
neural keel4.64e-3357
brain8.77e-3169
future brain8.77e-3169
neurectoderm1.12e-2990
neural plate3.54e-2986
presumptive neural plate3.54e-2986
regional part of brain4.72e-2959
ectoderm5.74e-29173
presumptive ectoderm5.74e-29173
ectoderm-derived structure3.05e-28169
anterior neural tube1.69e-2642
regional part of forebrain3.28e-2641
forebrain3.28e-2641
future forebrain3.28e-2641
anterior region of body2.03e-23129
craniocervical region2.03e-23129
head5.55e-23123
pre-chordal neural plate2.91e-2261
telencephalon1.08e-2134
gray matter1.11e-2134
brain grey matter1.11e-2134
regional part of telencephalon4.63e-2133
cerebral hemisphere1.29e-2032
cerebral cortex3.21e-1625
pallium3.21e-1625
regional part of cerebral cortex1.13e-1522
neocortex1.91e-1420
organism subdivision4.45e-11365
organ part5.27e-09219
multi-tissue structure2.44e-08347
posterior neural tube9.03e-0815
chordal neural plate9.03e-0815
organ1.61e-07511
basal ganglion4.54e-079
nuclear complex of neuraxis4.54e-079
aggregate regional part of brain4.54e-079
collection of basal ganglia4.54e-079
cerebral subcortex4.54e-079
nucleus of brain6.41e-079
neural nucleus6.41e-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
NFE2#477849.08285419430930.0009550740562778870.00687530875128248
NFYB#480173.450545669845740.003464355374716030.0176005161735646
NR2C2#718254.796266309594250.0035854275935850.0181608454554743
POLR2A#5430251.579009688645640.001311399023867790.0087846323297882
TBP#6908171.853385343548190.003537559862006710.0179497262026002
YY1#7528131.877800580826470.01261189534539230.0456021928395452
ZEB1#693573.477030121259030.003320156863606250.017172833928198



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.