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Difference between revisions of "Coexpression cluster:C1680"

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|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148915863756326!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298698129430864!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322555651509439!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572747913677329!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673740145466063!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00880775326156192!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.0329460874094272!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402160343075629!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238845825789906!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247844382752982!SIX5#147912;4:13.6693722843672:5.58844770365977e-05:0.0009374428039231!SRF#6722;4:11.0377426097342:0.000129925581484675:0.00171005643411191!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135220134571724!THAP1#55145;2:12.5476578411405:0.00952843466738653:0.0358893605102128
 
|tf_chipseq_enrich=CCNT2#905;4:5.06896126157011:0.00270999809128077:0.0148915863756326!E2F1#1869;4:3.92591137190346:0.00721498454710636:0.0298698129430864!E2F6#1876;5:5.01715573169739:0.000314497859929779:0.00322555651509439!ELF1#1997;5:4.25809795880754:0.000714241693977684:0.00572747913677329!HEY1#23462;5:4.04011104310571:0.000928885220517799:0.00673740145466063!IRF1#3659;4:6.10973100285112:0.00131552526476799:0.00880775326156192!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.0329460874094272!NANOG#79923;2:11.6979113924051:0.0109116495195608:0.0402160343075629!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00238845825789906!SIN3A#25942;5:5.40888472681514:0.000215952267165727:0.00247844382752982!SIX5#147912;4:13.6693722843672:5.58844770365977e-05:0.0009374428039231!SRF#6722;4:11.0377426097342:0.000129925581484675:0.00171005643411191!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135220134571724!THAP1#55145;2:12.5476578411405:0.00952843466738653:0.0358893605102128
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,1.16078,0.621241,0.778743,0.752887,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.167776,0.500405,0.384437,1.55551,0.44943,0.549618,0.802434,0.700122,0.642741,0.458349,0.659743,0.598009,1.00172,0.359091,0.27659,0.417272,0.757784,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,0.414516,0.451846,0.218848,1.32072,0.734485,0.609718,0.393318,1.16046,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,1.39076,0.330474,0.189341,1.23387,1.36104,0.709554,0.675933,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.963115,0.647361,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.99322,0.780629,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,2.6759,0.596731,0.897476,0.968277,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.629991,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,0.577088,0.363423,0.526389,1.29319,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,1.89906
 
}}
 
}}

Revision as of 06:02, 26 November 2012


Full id: C1680_Neutrophils_Eosinophils_pineal_optic_cerebellum_pituitary_parietal



Phase1 CAGE Peaks

Hg19::chr12:62860581..62860620,+p1@MON2
Hg19::chr1:12290063..12290118,+p1@VPS13D
Hg19::chr4:123073464..123073547,+p1@KIAA1109
Hg19::chr6:38607673..38607749,-p1@BTBD9
Hg19::chr8:9413410..9413451,+p1@TNKS


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:0008104protein localization0.0113683186556758
GO:0033036macromolecule localization0.0113683186556758
GO:0018107peptidyl-threonine phosphorylation0.0113683186556758
GO:0018210peptidyl-threonine modification0.0113683186556758
GO:0006895Golgi to endosome transport0.0170257968800675
GO:0000139Golgi membrane0.0170257968800675
GO:0018209peptidyl-serine modification0.0170257968800675
GO:0018105peptidyl-serine phosphorylation0.0170257968800675
GO:0044431Golgi apparatus part0.0170257968800675
GO:0007004telomere maintenance via telomerase0.0257469581026292
GO:0006892post-Golgi vesicle-mediated transport0.0289068878369803
GO:0005794Golgi apparatus0.0312744347931803
GO:0032200telomere organization and biogenesis0.0312744347931803
GO:0000723telomere maintenance0.0312744347931803
GO:0000781chromosome, telomeric region0.0312744347931803
GO:0003950NAD+ ADP-ribosyltransferase activity0.0352887257354325
GO:0016197endosome transport0.0352887257354325
GO:0015031protein transport0.0352887257354325
GO:0046907intracellular transport0.035882627027328
GO:0045184establishment of protein localization0.035882627027328
GO:0012505endomembrane system0.0408007570046309
GO:0006278RNA-dependent DNA replication0.0408007570046309
GO:0051649establishment of cellular localization0.0408007570046309
GO:0065002intracellular protein transport across a membrane0.0408007570046309
GO:0051641cellular localization0.0408007570046309
GO:0016763transferase activity, transferring pentosyl groups0.0408007570046309
GO:0051028mRNA transport0.0408007570046309
GO:0004190aspartic-type endopeptidase activity0.0408007570046309
GO:0005643nuclear pore0.0408007570046309
GO:0048193Golgi vesicle transport0.0408007570046309
GO:0050658RNA transport0.0408007570046309
GO:0051236establishment of RNA localization0.0408007570046309
GO:0050657nucleic acid transport0.0408007570046309
GO:0006403RNA localization0.0408007570046309
GO:0046930pore complex0.0417767984157967
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0435294639387703
GO:0044453nuclear membrane part0.0451850483065894
GO:0018193peptidyl-amino acid modification0.0477275083872672
GO:0031090organelle membrane0.0477275083872672
GO:0051179localization0.0479964255474786



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>


Uber Anatomy
Ontology termp-valuen
adult organism6.43e-44114
neural tube9.72e-2756
neural rod9.72e-2756
future spinal cord9.72e-2756
neural keel9.72e-2756
regional part of nervous system5.13e-2553
regional part of brain5.13e-2553
regional part of forebrain2.15e-2341
forebrain2.15e-2341
anterior neural tube2.15e-2341
future forebrain2.15e-2341
central nervous system1.24e-2281
brain1.30e-2268
future brain1.30e-2268
nervous system3.11e-2289
brain grey matter2.05e-1934
gray matter2.05e-1934
telencephalon2.59e-1934
regional part of telencephalon3.20e-1832
cerebral hemisphere4.07e-1832
neurectoderm4.86e-1686
neural plate8.83e-1682
presumptive neural plate8.83e-1682
regional part of cerebral cortex5.58e-1522
cerebral cortex3.58e-1425
pallium3.58e-1425
neocortex1.07e-1320
pre-chordal neural plate1.55e-1261
ectoderm-derived structure8.12e-10171
ectoderm8.12e-10171
presumptive ectoderm8.12e-10171
ecto-epithelium1.43e-09104
structure with developmental contribution from neural crest2.81e-09132
hematopoietic system6.09e-0898
blood island6.09e-0898
organ system subdivision4.86e-07223
hemolymphoid system6.47e-07108
basal ganglion8.27e-079
nuclear complex of neuraxis8.27e-079
aggregate regional part of brain8.27e-079
collection of basal ganglia8.27e-079
cerebral subcortex8.27e-079
neural nucleus9.78e-079
nucleus of brain9.78e-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
CCNT2#90545.068961261570110.002709998091280770.0148915863756326
E2F1#186943.925911371903460.007214984547106360.0298698129430864
E2F6#187655.017155731697390.0003144978599297790.00322555651509439
ELF1#199754.258097958807540.0007142416939776840.00572747913677329
HEY1#2346254.040111043105710.0009288852205177990.00673740145466063
IRF1#365946.109731002851120.001315525264767990.00880775326156192
MXI1#460135.976942977255580.008653004889366880.0329460874094272
NANOG#79923211.69791139240510.01091164951956080.0402160343075629
NFKB1#479055.488063424193840.0002008162847462320.00238845825789906
SIN3A#2594255.408884726815140.0002159522671657270.00247844382752982
SIX5#147912413.66937228436725.58844770365977e-050.0009374428039231
SRF#6722411.03774260973420.0001299255814846750.00171005643411191
TAF1#687253.343046285745290.002394600090870310.0135220134571724
THAP1#55145212.54765784114050.009528434667386530.0358893605102128



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.