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Coexpression cluster:C1005: Difference between revisions

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|tf_chipseq_enrich=EBF1#1879;4:4.4532334232845:0.00765188499674898:0.0315149151027473!FOS#2353;4:4.4989776544472:0.00737448991622712:0.0304794155827632!GATA2#2624;4:6.372465866777:0.00204874075705145:0.0118937429641855!GATA3#2625;4:13.618258178603:0.000112839652281084:0.00154656961215015!JUN#3725;4:6.25641459616817:0.002194211754114:0.0126454740860784!MAFF#23764;3:21.1182586837294:0.000293010169114186:0.00310771697492805!MAFK#7975;3:10.1627749266862:0.00244557310713952:0.01376742182711!TRIM28#10155;4:9.29526252263126:0.000491498033342148:0.00439332104623593!USF2#7392;4:6.4960986925348:0.00190676081592817:0.0112204300684428
|tf_chipseq_enrich=EBF1#1879;4:4.4532334232845:0.00765188499674898:0.0315149151027473!FOS#2353;4:4.4989776544472:0.00737448991622712:0.0304794155827632!GATA2#2624;4:6.372465866777:0.00204874075705145:0.0118937429641855!GATA3#2625;4:13.618258178603:0.000112839652281084:0.00154656961215015!JUN#3725;4:6.25641459616817:0.002194211754114:0.0126454740860784!MAFF#23764;3:21.1182586837294:0.000293010169114186:0.00310771697492805!MAFK#7975;3:10.1627749266862:0.00244557310713952:0.01376742182711!TRIM28#10155;4:9.29526252263126:0.000491498033342148:0.00439332104623593!USF2#7392;4:6.4960986925348:0.00190676081592817:0.0112204300684428
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}}
}}

Revision as of 14:37, 26 November 2012


Full id: C1005_nonsmall_cerebellum_spinal_medulla_locus_small_thalamus



Phase1 CAGE Peaks

Hg19::chr11:82556854..82556872,-p3@PRCP
Hg19::chr12:41221946..41221953,+p16@CNTN1
Hg19::chr12:41221975..41221996,+p2@CNTN1
Hg19::chr12:41222004..41222020,+p4@CNTN1
Hg19::chr18:32073253..32073339,+p2@DTNA
Hg19::chr18:32073350..32073378,+p6@DTNA
Hg19::chr18:32073391..32073409,+p9@DTNA
Hg19::chr18:32073414..32073417,+p18@DTNA


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:0008322Pro-X carboxypeptidase activity0.0027375485694101
GO:0004188serine-type Pro-X carboxypeptidase activity0.0027375485694101
GO:0007274neuromuscular synaptic transmission0.0150520853554045
GO:0004185serine carboxypeptidase activity0.0150520853554045
GO:0006941striated muscle contraction0.0404727979551289
GO:0007219Notch signaling pathway0.0455600295114098



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
neural tube6.92e-8456
neural rod6.92e-8456
future spinal cord6.92e-8456
neural keel6.92e-8456
central nervous system1.50e-8181
nervous system6.07e-8089
regional part of nervous system1.99e-7753
regional part of brain1.99e-7753
brain3.65e-7068
future brain3.65e-7068
adult organism1.77e-66114
neural plate6.04e-6582
presumptive neural plate6.04e-6582
regional part of forebrain6.54e-6341
forebrain6.54e-6341
anterior neural tube6.54e-6341
future forebrain6.54e-6341
neurectoderm3.41e-6186
brain grey matter1.33e-5334
gray matter1.33e-5334
telencephalon2.83e-5334
ecto-epithelium7.87e-52104
cerebral hemisphere2.48e-4932
regional part of telencephalon2.52e-4932
pre-chordal neural plate7.97e-4661
ectoderm-derived structure4.52e-45171
ectoderm4.52e-45171
presumptive ectoderm4.52e-45171
regional part of cerebral cortex1.34e-4122
structure with developmental contribution from neural crest9.98e-41132
neocortex1.87e-3720
organ system subdivision3.86e-36223
cerebral cortex5.52e-3625
pallium5.52e-3625
tube7.29e-24192
anatomical cluster7.11e-23373
posterior neural tube5.29e-2115
chordal neural plate5.29e-2115
anatomical conduit3.26e-19240
neural nucleus3.75e-199
nucleus of brain3.75e-199
basal ganglion5.04e-199
nuclear complex of neuraxis5.04e-199
aggregate regional part of brain5.04e-199
collection of basal ganglia5.04e-199
cerebral subcortex5.04e-199
segmental subdivision of nervous system7.73e-1713
segmental subdivision of hindbrain3.88e-1512
hindbrain3.88e-1512
presumptive hindbrain3.88e-1512
telencephalic nucleus6.44e-157
epithelium8.01e-15306
brainstem1.46e-146
cell layer1.65e-14309
multi-tissue structure1.20e-13342
gyrus2.29e-136
organ part1.30e-12218
limbic system9.17e-125
embryo2.45e-11592
temporal lobe2.78e-116
parietal lobe3.77e-115
diencephalon8.97e-117
future diencephalon8.97e-117
developing anatomical structure9.84e-11581
occipital lobe1.07e-105
germ layer3.26e-10560
germ layer / neural crest3.26e-10560
embryonic tissue3.26e-10560
presumptive structure3.26e-10560
germ layer / neural crest derived structure3.26e-10560
epiblast (generic)3.26e-10560
embryonic structure5.50e-10564
organ1.19e-09503
regional part of metencephalon2.73e-099
metencephalon2.73e-099
future metencephalon2.73e-099
regional part of diencephalon2.86e-094
corpus striatum3.38e-094
striatum3.38e-094
ventral part of telencephalon3.38e-094
future corpus striatum3.38e-094
multi-cellular organism3.93e-09656
anatomical system4.99e-09624
anatomical group5.61e-09625
medulla oblongata3.45e-083
myelencephalon3.45e-083
future myelencephalon3.45e-083
pons4.74e-083
spinal cord7.41e-083
dorsal region element7.41e-083
dorsum7.41e-083
frontal cortex1.70e-073
caudate-putamen2.56e-073
dorsal striatum2.56e-073


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
EBF1#187944.45323342328450.007651884996748980.0315149151027473
FOS#235344.49897765444720.007374489916227120.0304794155827632
GATA2#262446.3724658667770.002048740757051450.0118937429641855
GATA3#2625413.6182581786030.0001128396522810840.00154656961215015
JUN#372546.256414596168170.0021942117541140.0126454740860784
MAFF#23764321.11825868372940.0002930101691141860.00310771697492805
MAFK#7975310.16277492668620.002445573107139520.01376742182711
TRIM28#1015549.295262522631260.0004914980333421480.00439332104623593
USF2#739246.49609869253480.001906760815928170.0112204300684428



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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