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Coexpression cluster:C1949: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.61e-26!115;UBERON:0005743!6.13e-21!86;UBERON:0000468!1.27e-19!659;UBERON:0001017!2.41e-19!82;UBERON:0003075!1.13e-18!86;UBERON:0007284!1.13e-18!86;UBERON:0000073!1.16e-18!94;UBERON:0001016!1.16e-18!94;UBERON:0001049!3.68e-18!57;UBERON:0005068!3.68e-18!57;UBERON:0006241!3.68e-18!57;UBERON:0007135!3.68e-18!57;UBERON:0002346!2.23e-17!90;UBERON:0002616!3.55e-17!59;UBERON:0000467!1.83e-16!625;UBERON:0000480!4.47e-16!626;UBERON:0003080!1.11e-15!42;UBERON:0000062!2.35e-15!511;UBERON:0002780!2.77e-15!41;UBERON:0001890!2.77e-15!41;UBERON:0006240!2.77e-15!41;UBERON:0000955!3.18e-15!69;UBERON:0006238!3.18e-15!69;UBERON:0003056!6.25e-15!61;UBERON:0004121!2.34e-14!169;UBERON:0000477!4.34e-14!286;UBERON:0000922!4.82e-14!612;UBERON:0004111!6.05e-14!241;UBERON:0000481!7.49e-14!347;UBERON:0000924!1.03e-13!173;UBERON:0006601!1.03e-13!173;UBERON:0000033!3.39e-13!123;UBERON:0000475!8.73e-13!365;UBERON:0002050!1.87e-12!605;UBERON:0005423!1.87e-12!605;UBERON:0000025!2.39e-12!194;UBERON:0000923!2.41e-12!604;UBERON:0005291!2.41e-12!604;UBERON:0006598!2.41e-12!604;UBERON:0002532!2.41e-12!604;UBERON:0000119!2.98e-12!312;UBERON:0000483!3.02e-12!309;UBERON:0000153!4.75e-12!129;UBERON:0007811!4.75e-12!129;UBERON:0001893!1.18e-11!34;UBERON:0002020!1.43e-11!34;UBERON:0003528!1.43e-11!34;UBERON:0002791!3.05e-11!33;UBERON:0001869!3.16e-11!32;UBERON:0000064!2.99e-10!219;UBERON:0000956!2.71e-08!25;UBERON:0000203!2.71e-08!25;UBERON:0002619!2.37e-07!22;UBERON:0001950!6.27e-07!20
|ontology_enrichment_uberon=UBERON:0007023!2.61e-26!115;UBERON:0005743!6.13e-21!86;UBERON:0000468!1.27e-19!659;UBERON:0001017!2.41e-19!82;UBERON:0003075!1.13e-18!86;UBERON:0007284!1.13e-18!86;UBERON:0000073!1.16e-18!94;UBERON:0001016!1.16e-18!94;UBERON:0001049!3.68e-18!57;UBERON:0005068!3.68e-18!57;UBERON:0006241!3.68e-18!57;UBERON:0007135!3.68e-18!57;UBERON:0002346!2.23e-17!90;UBERON:0002616!3.55e-17!59;UBERON:0000467!1.83e-16!625;UBERON:0000480!4.47e-16!626;UBERON:0003080!1.11e-15!42;UBERON:0000062!2.35e-15!511;UBERON:0002780!2.77e-15!41;UBERON:0001890!2.77e-15!41;UBERON:0006240!2.77e-15!41;UBERON:0000955!3.18e-15!69;UBERON:0006238!3.18e-15!69;UBERON:0003056!6.25e-15!61;UBERON:0004121!2.34e-14!169;UBERON:0000477!4.34e-14!286;UBERON:0000922!4.82e-14!612;UBERON:0004111!6.05e-14!241;UBERON:0000481!7.49e-14!347;UBERON:0000924!1.03e-13!173;UBERON:0006601!1.03e-13!173;UBERON:0000033!3.39e-13!123;UBERON:0000475!8.73e-13!365;UBERON:0002050!1.87e-12!605;UBERON:0005423!1.87e-12!605;UBERON:0000025!2.39e-12!194;UBERON:0000923!2.41e-12!604;UBERON:0005291!2.41e-12!604;UBERON:0006598!2.41e-12!604;UBERON:0002532!2.41e-12!604;UBERON:0000119!2.98e-12!312;UBERON:0000483!3.02e-12!309;UBERON:0000153!4.75e-12!129;UBERON:0007811!4.75e-12!129;UBERON:0001893!1.18e-11!34;UBERON:0002020!1.43e-11!34;UBERON:0003528!1.43e-11!34;UBERON:0002791!3.05e-11!33;UBERON:0001869!3.16e-11!32;UBERON:0000064!2.99e-10!219;UBERON:0000956!2.71e-08!25;UBERON:0000203!2.71e-08!25;UBERON:0002619!2.37e-07!22;UBERON:0001950!6.27e-07!20
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}}
}}

Revision as of 12:42, 5 September 2012


Full id: C1949_mature_liver_Hepatocyte_seminal_ductus_pineal_immature



Phase1 CAGE Peaks

Hg19::chr5:115152347..115152363,-p1@CDO1
Hg19::chr9:130860731..130860742,+p6@SLC25A25
Hg19::chr9:130860748..130860774,+p5@SLC25A25
Hg19::chr9:130860779..130860800,+p3@SLC25A25
Hg19::chr9:130860810..130860828,+p2@SLC25A25


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:0046439L-cysteine metabolic process0.00103026021429412
GO:0019530taurine metabolic process0.00103026021429412
GO:0017172cysteine dioxygenase activity0.00103026021429412
GO:0042412taurine biosynthetic process0.00103026021429412
GO:0006534cysteine metabolic process0.00494488509694741
GO:0000097sulfur amino acid biosynthetic process0.013732961356353
GO:0000096sulfur amino acid metabolic process0.0170658475389813
GO:0042398amino acid derivative biosynthetic process0.0205918601248543
GO:0044272sulfur compound biosynthetic process0.0205918601248543
GO:0009069serine family amino acid metabolic process0.0226477100970827
GO:0051213dioxygenase activity0.023150489273369
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.023150489273369
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.023150489273369
GO:0008652amino acid biosynthetic process0.023150489273369
GO:0006790sulfur metabolic process0.023150489273369
GO:0006575amino acid derivative metabolic process0.023150489273369
GO:0009309amine biosynthetic process0.0287971847411023
GO:0044271nitrogen compound biosynthetic process0.0335828456911871



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 cell1.91e-0715
Uber Anatomy
Ontology termp-valuen
adult organism2.61e-26115
multi-cellular organism1.27e-19659
central nervous system2.41e-1982
neural plate1.13e-1886
presumptive neural plate1.13e-1886
regional part of nervous system1.16e-1894
nervous system1.16e-1894
neural tube3.68e-1857
neural rod3.68e-1857
future spinal cord3.68e-1857
neural keel3.68e-1857
neurectoderm2.23e-1790
regional part of brain3.55e-1759
anatomical system1.83e-16625
anatomical group4.47e-16626
anterior neural tube1.11e-1542
organ2.35e-15511
regional part of forebrain2.77e-1541
forebrain2.77e-1541
future forebrain2.77e-1541
brain3.18e-1569
future brain3.18e-1569
pre-chordal neural plate6.25e-1561
ectoderm-derived structure2.34e-14169
anatomical cluster4.34e-14286
embryo4.82e-14612
anatomical conduit6.05e-14241
multi-tissue structure7.49e-14347
ectoderm1.03e-13173
presumptive ectoderm1.03e-13173
head3.39e-13123
organism subdivision8.73e-13365
embryonic structure1.87e-12605
developing anatomical structure1.87e-12605
tube2.39e-12194
germ layer2.41e-12604
embryonic tissue2.41e-12604
presumptive structure2.41e-12604
epiblast (generic)2.41e-12604
cell layer2.98e-12312
epithelium3.02e-12309
anterior region of body4.75e-12129
craniocervical region4.75e-12129
telencephalon1.18e-1134
gray matter1.43e-1134
brain grey matter1.43e-1134
regional part of telencephalon3.05e-1133
cerebral hemisphere3.16e-1132
organ part2.99e-10219
cerebral cortex2.71e-0825
pallium2.71e-0825
regional part of cerebral cortex2.37e-0722
neocortex6.27e-0720


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
BRCA1#672416.1473845145792.89130901545765e-050.000605262421858852
CEBPB#105146.376918100659850.001113944176677320.0076584303777238
E2F4#1874410.13444825222760.0001818201509632970.00220368048583681
EP300#203356.77394172622327.00901578206049e-050.0011097856265352
FOSL2#2355413.54416048364945.7953819349229e-050.000965179228036059
GTF2F1#2962410.19172870140610.000177833889427640.0021596271602248
HEY1#2346254.040111043105710.0009288852205177990.00674818054713818
HNF4A#3172418.5058322903631.68463364181741e-050.000387877982622947
HNF4G#3174423.00273802115747.10515202727268e-060.000204874371224829
HSF1#32974131.4325333333336.79362350565572e-095.3267210608647e-07
IRF3#3661437.58556176919171.00727027008258e-064.25215439519621e-05
JUN#3725410.01026335386910.0001908531347801070.00230620277025333
JUND#372745.595731153496820.001849593301755460.0109382601835809
MAX#414945.16204440720570.002526309009485180.0140037782836167
MXI1#460147.969257303007440.0004668546380070170.00429622271026653
MYC#460944.177825497287520.005691969036823440.0256909786177797
NFYA#4800414.74046455986444.14733626928016e-050.000752508083091297
NFYB#4801413.40783460282926.03169250119439e-050.000991881488162873
RFX5#599349.638328661756080.000221480125815720.00249823553948244
SIN3A#2594244.327107781452110.004977052855762880.0232499182897088
SP1#666744.558705102512720.00407573565781680.019491975289254
STAT3#677448.415571997723390.0003771527211598630.0037446005366684
TAF1#687253.343046285745290.002394600090870310.0135535247610234
TBP#690853.706770687096390.001428755106721120.00920131680279011
TFAP2C#702248.647382887888180.0003390518878174050.00344927334032359
ZNF263#1012758.221841637010682.6606316672286e-050.000572345439121912



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.