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Coexpression cluster:C1942: Difference between revisions

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|tf_chipseq_enrich=SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714394445147779!STAT3#6774;4:8.41557199772339:0.000377152721159863:0.00374424458604705
|tf_chipseq_enrich=SPI1#6688;4:6.56345880681818:0.000995742963645402:0.00714394445147779!STAT3#6774;4:8.41557199772339:0.000377152721159863:0.00374424458604705
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}}
}}

Revision as of 15:12, 26 November 2012


Full id: C1942_Neural_spinal_Astrocyte_Neurons_caudate_locus_medial



Phase1 CAGE Peaks

Hg19::chr4:57547751..57547764,-p6@HOPX
Hg19::chr4:57547773..57547780,-p12@HOPX
Hg19::chr4:57547820..57547829,-p8@HOPX
Hg19::chr4:57547870..57547873,-p11@HOPX
Hg19::chr6:111894900..111894919,-p13@TRAF3IP2


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:0043416regulation of skeletal muscle regeneration0.00104792181796774
GO:0051153regulation of striated muscle cell differentiation0.00104792181796774
GO:0043415positive regulation of skeletal muscle regeneration0.00104792181796774
GO:0051149positive regulation of muscle cell differentiation0.00104792181796774
GO:0051155positive regulation of striated muscle cell differentiation0.00104792181796774
GO:0051147regulation of muscle cell differentiation0.0029939301333032
GO:0043403skeletal muscle regeneration0.0029939301333032
GO:0048522positive regulation of cellular process0.00785744710401431
GO:0051146striated muscle cell differentiation0.00785744710401431
GO:0042246tissue regeneration0.00785744710401431
GO:0048518positive regulation of biological process0.00785744710401431
GO:0031099regeneration0.00785744710401431
GO:0048589developmental growth0.0149048318470955
GO:0042692muscle cell differentiation0.0164063264175261
GO:0045597positive regulation of cell differentiation0.0164063264175261
GO:0051094positive regulation of developmental process0.0222463790385095
GO:0014706striated muscle development0.0270879516452688
GO:0007507heart development0.0272617417255358
GO:0043123positive regulation of I-kappaB kinase/NF-kappaB cascade0.0272617417255358
GO:0043122regulation of I-kappaB kinase/NF-kappaB cascade0.0282493298120415
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0311397934867029
GO:0042060wound healing0.0311397934867029
GO:0007249I-kappaB kinase/NF-kappaB cascade0.0313714865634195
GO:0045595regulation of cell differentiation0.0313714865634195
GO:0009967positive regulation of signal transduction0.0319946685882814
GO:0007517muscle development0.0345747901444914
GO:0045892negative regulation of transcription, DNA-dependent0.0392769744282824
GO:0016564transcription repressor activity0.0399200397743542
GO:0050793regulation of developmental process0.0424920942631532



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
astrocyte of the cerebral cortex3.05e-103
acinar cell of salivary gland1.68e-083
Uber Anatomy
Ontology termp-valuen
neural tube5.24e-10056
neural rod5.24e-10056
future spinal cord5.24e-10056
neural keel5.24e-10056
central nervous system1.76e-9381
regional part of nervous system3.82e-9153
regional part of brain3.82e-9153
nervous system5.10e-8389
brain grey matter2.97e-7934
gray matter2.97e-7934
telencephalon3.58e-7934
regional part of forebrain1.42e-7741
forebrain1.42e-7741
anterior neural tube1.42e-7741
future forebrain1.42e-7741
brain5.85e-7568
future brain5.85e-7568
cerebral hemisphere3.68e-7432
regional part of telencephalon1.13e-7332
neural plate8.67e-6882
presumptive neural plate8.67e-6882
neurectoderm4.20e-6486
cerebral cortex6.91e-5625
pallium6.91e-5625
pre-chordal neural plate2.68e-5261
adult organism4.49e-52114
ecto-epithelium5.36e-51104
regional part of cerebral cortex2.30e-4722
ectoderm-derived structure2.30e-44171
ectoderm2.30e-44171
presumptive ectoderm2.30e-44171
structure with developmental contribution from neural crest1.48e-43132
neocortex7.74e-4220
organ system subdivision4.75e-35223
neural nucleus2.49e-249
nucleus of brain2.49e-249
basal ganglion3.12e-249
nuclear complex of neuraxis3.12e-249
aggregate regional part of brain3.12e-249
collection of basal ganglia3.12e-249
cerebral subcortex3.12e-249
tube2.00e-23192
posterior neural tube2.19e-2215
chordal neural plate2.19e-2215
anatomical conduit2.61e-19240
telencephalic nucleus6.07e-197
anatomical cluster5.06e-18373
gyrus6.13e-186
brainstem1.10e-176
limbic system4.01e-155
temporal lobe7.95e-156
segmental subdivision of hindbrain1.20e-1412
hindbrain1.20e-1412
presumptive hindbrain1.20e-1412
segmental subdivision of nervous system2.09e-1313
organ part5.87e-13218
epithelium1.60e-12306
cell layer2.77e-12309
corpus striatum5.44e-124
striatum5.44e-124
ventral part of telencephalon5.44e-124
future corpus striatum5.44e-124
multi-tissue structure5.23e-11342
spinal cord1.70e-103
dorsal region element1.70e-103
dorsum1.70e-103
parietal lobe6.35e-105
frontal cortex7.07e-103
occipital lobe8.37e-105
medulla oblongata8.71e-103
myelencephalon8.71e-103
future myelencephalon8.71e-103
pons1.31e-093
caudate-putamen1.92e-093
dorsal striatum1.92e-093
germ layer7.08e-09560
germ layer / neural crest7.08e-09560
embryonic tissue7.08e-09560
presumptive structure7.08e-09560
germ layer / neural crest derived structure7.08e-09560
epiblast (generic)7.08e-09560
embryonic structure1.04e-08564
organ1.11e-08503
embryo3.48e-08592
developing anatomical structure5.14e-08581
regional part of metencephalon5.70e-089
metencephalon5.70e-089
future metencephalon5.70e-089
Ammon's horn2.87e-072
lobe parts of cerebral cortex2.87e-072
hippocampal formation2.87e-072
limbic lobe2.87e-072
locus ceruleus4.38e-072
brainstem nucleus4.38e-072
hindbrain nucleus4.38e-072
middle temporal gyrus4.94e-072
caudate nucleus5.09e-072
future caudate nucleus5.09e-072


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
SPI1#668846.563458806818180.0009957429636454020.00714394445147779
STAT3#677448.415571997723390.0003771527211598630.00374424458604705



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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