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Coexpression cluster:C1171: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic
|full_id=C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic
|gostat_on_coexpression_clusters=GO:0008026!ATP-dependent helicase activity!0.0126628131237378!10856;22907$GO:0017111!nucleoside-triphosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016462!pyrophosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016818!hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides!0.0126628131237378!10856;55210;22907$GO:0016817!hydrolase activity, acting on acid anhydrides!0.0126628131237378!10856;55210;22907$GO:0005524!ATP binding!0.0126628131237378!10856;55210;7407;22907$GO:0032559!adenyl ribonucleotide binding!0.0126628131237378!10856;55210;7407;22907$GO:0030554!adenyl nucleotide binding!0.0130157929178116!10856;55210;7407;22907$GO:0004386!helicase activity!0.015254011509818!10856;22907$GO:0035267!NuA4 histone acetyltransferase complex!0.015254011509818!10856$GO:0043189!H4/H2A histone acetyltransferase complex!0.0159176240429507!10856$GO:0032553!ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0032555!purine ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0017076!purine nucleotide binding!0.0170004643870686!10856;55210;7407;22907$GO:0000123!histone acetyltransferase complex!0.0194313746840619!10856$GO:0004832!valine-tRNA ligase activity!0.0194313746840619!7407$GO:0006438!valyl-tRNA aminoacylation!0.0194313746840619!7407$GO:0000166!nucleotide binding!0.0240891554983028!10856;55210;7407;22907$GO:0042623!ATPase activity, coupled!0.0262980976105518!10856;22907$GO:0016887!ATPase activity!0.0348302374230744!10856;22907$GO:0046822!regulation of nucleocytoplasmic transport!0.0348302374230744!8086$GO:0043231!intracellular membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0043227!membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0004003!ATP-dependent DNA helicase activity!0.0369966852587803!10856$GO:0016363!nuclear matrix!0.0459929166824502!10856$GO:0003678!DNA helicase activity!0.0459929166824502!10856$GO:0003684!damaged DNA binding!0.0459929166824502!10856$GO:0003725!double-stranded RNA binding!0.0479566301137395!22907
|gostat_on_coexpression_clusters=GO:0008026!ATP-dependent helicase activity!0.0126628131237378!10856;22907$GO:0017111!nucleoside-triphosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016462!pyrophosphatase activity!0.0126628131237378!10856;55210;22907$GO:0016818!hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides!0.0126628131237378!10856;55210;22907$GO:0016817!hydrolase activity, acting on acid anhydrides!0.0126628131237378!10856;55210;22907$GO:0005524!ATP binding!0.0126628131237378!10856;55210;7407;22907$GO:0032559!adenyl ribonucleotide binding!0.0126628131237378!10856;55210;7407;22907$GO:0030554!adenyl nucleotide binding!0.0130157929178116!10856;55210;7407;22907$GO:0004386!helicase activity!0.015254011509818!10856;22907$GO:0035267!NuA4 histone acetyltransferase complex!0.015254011509818!10856$GO:0043189!H4/H2A histone acetyltransferase complex!0.0159176240429507!10856$GO:0032553!ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0032555!purine ribonucleotide binding!0.0159176240429507!10856;55210;7407;22907$GO:0017076!purine nucleotide binding!0.0170004643870686!10856;55210;7407;22907$GO:0000123!histone acetyltransferase complex!0.0194313746840619!10856$GO:0004832!valine-tRNA ligase activity!0.0194313746840619!7407$GO:0006438!valyl-tRNA aminoacylation!0.0194313746840619!7407$GO:0000166!nucleotide binding!0.0240891554983028!10856;55210;7407;22907$GO:0042623!ATPase activity, coupled!0.0262980976105518!10856;22907$GO:0016887!ATPase activity!0.0348302374230744!10856;22907$GO:0046822!regulation of nucleocytoplasmic transport!0.0348302374230744!8086$GO:0043231!intracellular membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0043227!membrane-bound organelle!0.0348302374230744!10856;26155;7407;8086;22907$GO:0004003!ATP-dependent DNA helicase activity!0.0369966852587803!10856$GO:0016363!nuclear matrix!0.0459929166824502!10856$GO:0003678!DNA helicase activity!0.0459929166824502!10856$GO:0003684!damaged DNA binding!0.0459929166824502!10856$GO:0003725!double-stranded RNA binding!0.0479566301137395!22907

Revision as of 13:39, 12 September 2012


Full id: C1171_Alveolar_Renal_Bronchial_Mesenchymal_Smooth_Keratinocyte_embryonic



Phase1 CAGE Peaks

Hg19::chr12:53715328..53715411,-p1@AAAS
Hg19::chr19:49497121..49497164,+p1@RUVBL2
Hg19::chr1:1447517..1447556,+p1@ATAD3A
Hg19::chr1:894620..894659,-p1@NOC2L
Hg19::chr3:47866490..47866534,+p1@DHX30
Hg19::chr6:31763408..31763545,-p1@VARS
Hg19::chr7:1177874..1177936,-p2@C7orf50


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:0008026ATP-dependent helicase activity0.0126628131237378
GO:0017111nucleoside-triphosphatase activity0.0126628131237378
GO:0016462pyrophosphatase activity0.0126628131237378
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0126628131237378
GO:0016817hydrolase activity, acting on acid anhydrides0.0126628131237378
GO:0005524ATP binding0.0126628131237378
GO:0032559adenyl ribonucleotide binding0.0126628131237378
GO:0030554adenyl nucleotide binding0.0130157929178116
GO:0004386helicase activity0.015254011509818
GO:0035267NuA4 histone acetyltransferase complex0.015254011509818
GO:0043189H4/H2A histone acetyltransferase complex0.0159176240429507
GO:0032553ribonucleotide binding0.0159176240429507
GO:0032555purine ribonucleotide binding0.0159176240429507
GO:0017076purine nucleotide binding0.0170004643870686
GO:0000123histone acetyltransferase complex0.0194313746840619
GO:0004832valine-tRNA ligase activity0.0194313746840619
GO:0006438valyl-tRNA aminoacylation0.0194313746840619
GO:0000166nucleotide binding0.0240891554983028
GO:0042623ATPase activity, coupled0.0262980976105518
GO:0016887ATPase activity0.0348302374230744
GO:0046822regulation of nucleocytoplasmic transport0.0348302374230744
GO:0043231intracellular membrane-bound organelle0.0348302374230744
GO:0043227membrane-bound organelle0.0348302374230744
GO:0004003ATP-dependent DNA helicase activity0.0369966852587803
GO:0016363nuclear matrix0.0459929166824502
GO:0003678DNA helicase activity0.0459929166824502
GO:0003684damaged DNA binding0.0459929166824502
GO:0003725double-stranded RNA binding0.0479566301137395



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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell2.81e-24254
embryonic cell1.54e-23248
animal cell3.05e-22679
eukaryotic cell3.05e-22679
non-terminally differentiated cell6.46e-16180
mesodermal cell2.15e-14119
contractile cell1.01e-1059
native cell4.89e-10722
electrically responsive cell8.45e-1060
electrically active cell8.45e-1060
muscle cell1.37e-0854
muscle precursor cell3.71e-0857
myoblast3.71e-0857
multi-potent skeletal muscle stem cell3.71e-0857
somatic cell4.15e-08591
epithelial cell of nephron9.46e-0816
smooth muscle cell1.72e-0742
smooth muscle myoblast1.72e-0742
squamous epithelial cell1.80e-0762
meso-epithelial cell5.81e-0744
blood vessel endothelial cell7.45e-0718
embryonic blood vessel endothelial progenitor cell7.45e-0718
kidney cortical cell7.67e-0713
renal cortical epithelial cell7.67e-0713
endothelial cell9.48e-0735
Uber Anatomy
Ontology termp-valuen
epithelial tube9.30e-15118
mesenchyme8.64e-14238
entire embryonic mesenchyme8.64e-14238
unilaminar epithelium1.55e-11138
cell layer3.94e-11312
trunk mesenchyme8.96e-11143
vasculature9.14e-1179
vascular system9.14e-1179
trunk1.68e-10216
epithelium1.90e-10309
blood vessel1.93e-1060
epithelial tube open at both ends1.93e-1060
blood vasculature1.93e-1060
vascular cord1.93e-1060
vessel2.02e-1069
multilaminar epithelium2.88e-1082
dermomyotome3.96e-1070
artery7.01e-1042
arterial blood vessel7.01e-1042
arterial system7.01e-1042
splanchnic layer of lateral plate mesoderm1.61e-0984
somite2.29e-0883
paraxial mesoderm2.29e-0883
presomitic mesoderm2.29e-0883
presumptive segmental plate2.29e-0883
trunk paraxial mesoderm2.29e-0883
presumptive paraxial mesoderm2.29e-0883
primordium4.90e-08168
nephron epithelium9.46e-0816
nephron9.46e-0816
uriniferous tubule9.46e-0816
metanephric mesenchyme9.46e-0816
nephrogenic mesenchyme9.46e-0816
skeletal muscle tissue1.11e-0761
striated muscle tissue1.11e-0761
myotome1.11e-0761
simple squamous epithelium3.55e-0722
multi-tissue structure5.77e-07347
excretory tube6.83e-0717
mesonephric epithelium6.83e-0717
mesonephric tubule6.83e-0717
nephric duct6.83e-0717
kidney epithelium6.83e-0717
renal duct6.83e-0717
mesonephric duct6.83e-0717
pronephric duct6.83e-0717
endothelium7.45e-0718
blood vessel endothelium7.45e-0718
cardiovascular system endothelium7.45e-0718
cortex of kidney7.67e-0713
renal parenchyma7.67e-0713
muscle tissue8.04e-0763
musculature8.04e-0763
musculature of body8.04e-0763
Disease
Ontology termp-valuen
cancer1.61e-17235
disease of cellular proliferation3.47e-17239
hematologic cancer1.63e-0951
immune system cancer1.63e-0951
organ system cancer1.04e-08137
cell type cancer1.72e-08143
leukemia4.37e-0839
carcinoma2.35e-07106
myeloid leukemia4.89e-0731


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
BCLAF1#977439.279706118623640.00299499233575710.0159207005931764
CCNT2#90565.431029923110839.35028339706757e-050.00135818393283218
CHD2#110657.38858773865490.0001498689600820670.00193212743142958
CTCF#1066453.828754552196450.003387371192681340.0172926806135715
CTCFL#140690411.28369963369960.0002032736265059930.00241356233272617
E2F1#186953.505278010628090.005090553587915050.0236879489470798
E2F4#1874610.85833741310091.57765285246789e-066.00249494567919e-05
EGR1#195864.275582081265830.0003762130619866450.00373633662807372
ELF1#199774.258097958807543.93848941900192e-050.000735046276681812
ELK4#200549.277532376267440.0004328178589665770.00404212325606817
ETS1#211379.728760922202341.21106237796078e-076.97640064488944e-06
FOSL1#8061211.34673706182090.01223664790675720.0443636362944358
GABPB1#255377.067683836182171.13438576906404e-064.65700138896537e-05
GTF2F1#296235.459854661467560.0132988216841570.0470245001987972
HDAC2#306647.666068706643580.0008986373447057820.00668609999599111
HEY1#2346263.462952322662040.001267890095872120.00850572801405375
HMGN3#932455.841819802393280.0004629187191299590.00426338343097123
IRF1#365944.364093573465090.00739345582427820.0305505492712875
IRF3#3661213.42341491756850.00885816023056540.0336144682915493
MAX#414954.608968220719370.001424337014033610.00917909005360088
MXI1#460157.115408306256640.0001797256225248230.00217905320302647
MYC#460975.22228187160949.4355989882785e-060.000250940800289487
NFKB1#479075.488063424193846.66568321176054e-060.000194620433031328
NFYB#480137.182768537229910.00619473990889960.0273746484448492
PAX5#507954.763975379412740.001218821047007470.00819919171197507
POLR2A#543072.147453176558070.004747636447610280.0223310395852986
REST#597845.514302123501730.003115641375761960.0163761685779166
SIN3A#2594275.408884726815147.3795239773719e-060.000211501126419523
SIX5#14791249.763837345976570.0003555371351068720.00355908586728904
SMARCC1#6599212.47524551989470.01020047316571840.0379890602629699
SMC3#912636.447828362114080.008384311283437850.0329451479036444
SP1#666764.884326895549340.0001736361122290910.00211307176941202
SP2#6668414.94487456791126.81071539656055e-050.00108795396956468
SRF#672247.884101864095890.0008074788728092760.0061659929807215
STAT1#677238.874251784513940.003402369532693760.0173590655410358
TAF1#687273.343046285745290.0002142336319622450.0024649494644161
TAF7#687946.533182517099380.00164849410947510.0103118756767771
TBP#690873.706770687096390.0001039672097505110.00145066552025834
TFAP2A#702037.079414731304980.006452554472180970.0280288789468913
TFAP2C#702257.720877578471590.0001211811995604330.00164193607951376
THAP1#55145313.44391911550770.001029040833692380.00728920209102
TRIM28#1015537.967367876541080.004622341263156460.0218321589717256
USF1#739154.543928055148540.001522788355968760.00970397785764972
YY1#752874.911170749853861.45048003565243e-050.000345308147808306
ZBTB7A#5134166.301636549607913.91424956694869e-050.000731306458895446
ZNF143#7702611.57217990190961.08146108094101e-064.4980770144324e-05
ZNF263#1012744.698195221148960.00564122953609810.0254839902902612



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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