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Difference between revisions of "Coexpression cluster:C2719"

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|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360246159307874!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296290999808435!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0173042146862622!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199893647568878!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0419095880072193!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000614795479676533!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722972208626903!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320153922763543!JUNB#3726;3:22.9579744948659:0.000135977250401878:0.00177961504445135!MAFK#7975;3:20.3255498533724:0.000195321368893111:0.00235121812423094!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224511752453964!MEF2C#4208;4:41.3113544926241:3.42889182145094e-07:1.69881419801003e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768698634424122!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435129107007617!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188516174738727!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195874294870041!SP1#6667;4:5.6983813781409:0.000948260606533398:0.006851289483621!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.0024968262453813!STAT2#6773;3:48.9478283898305:1.42094046481278e-05:0.000340448729535631!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.0167431961988741!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032284486692235!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188930021314063!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244701792788437!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230634062095639
 
|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360246159307874!BCL11A#53335;2:14.1847275518035:0.00710832858529874:0.0296290999808435!CHD2#1106;3:7.75801712558764:0.00335152246453634:0.0173042146862622!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00199893647568878!EP300#2033;3:5.0804562946674:0.0114429840539824:0.0419095880072193!GATA1#2623;4:13.5603081438004:2.95627390049268e-05:0.000614795479676533!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000722972208626903!IRF1#3659;3:5.72787281517293:0.00809711479033333:0.0320153922763543!JUNB#3726;3:22.9579744948659:0.000135977250401878:0.00177961504445135!MAFK#7975;3:20.3255498533724:0.000195321368893111:0.00235121812423094!MEF2A#4205;4:18.7432309096441:8.0978922767748e-06:0.000224511752453964!MEF2C#4208;4:41.3113544926241:3.42889182145094e-07:1.69881419801003e-05!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768698634424122!PAX5#5079;3:5.00217414838337:0.0119653317478641:0.0435129107007617!POU2F2#5452;4:9.10612405774252:0.00014539566517493:0.00188516174738727!REST#5978;3:7.23752153709602:0.00410469730419261:0.0195874294870041!SP1#6667;4:5.6983813781409:0.000948260606533398:0.006851289483621!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.0024968262453813!STAT2#6773;3:48.9478283898305:1.42094046481278e-05:0.000340448729535631!STAT3#6774;3:7.88959874786568:0.00319076048168013:0.0167431961988741!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.032284486692235!TAL1#6886;3:22.4014625080802:0.000146275639593017:0.00188930021314063!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244701792788437!TRIM28#10155;4:18.5905250452625:8.36730015875654e-06:0.000230634062095639
 
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 +
|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,1.75588,2.27411,1.75218,1.92131,0.395818,0.392841,0.151681,1.68405,2.01638,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,1.3102,0.632849,0.892087,0.316693,1.72987,0.537869,0.297585,0.682839,1.09415,1.10579,0.344471,1.23824,0.285913,0.491074,0.740899,1.17228,0.371755,0.493145,0.66492,1.03152,0.53106,0.0946706,0.61613,0.822818,1.65941,0.515703,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.859396,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,1.966,0.535192,0.456994,0.354969,1.15558,0.939507,0.272395,2.04634,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,1.40954,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,1.64086,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,2.24704,0.768101,0.963351,2.1895,0.661255,1.11576,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987
 
}}
 
}}

Revision as of 06:40, 26 November 2012


Full id: C2719_CD14_CD34_immature_CD133_acute_Macrophage_pharyngeal



Phase1 CAGE Peaks

Hg19::chr3:130569347..130569360,+p13@ATP2C1
Hg19::chr3:130569381..130569392,+p15@ATP2C1
Hg19::chr3:130569523..130569576,+p8@ATP2C1
Hg19::chr3:130569592..130569620,+p5@ATP2C1


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


No GOStat results

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
myeloid cell3.36e-41108
common myeloid progenitor3.36e-41108
hematopoietic stem cell5.29e-33168
angioblastic mesenchymal cell5.29e-33168
hematopoietic cell1.99e-32177
granulocyte monocyte progenitor cell4.61e-3267
myeloid lineage restricted progenitor cell1.15e-3066
hematopoietic oligopotent progenitor cell1.45e-30161
hematopoietic multipotent progenitor cell1.45e-30161
macrophage dendritic cell progenitor3.38e-2861
myeloid leukocyte6.38e-2872
monopoietic cell1.54e-2659
monocyte1.54e-2659
monoblast1.54e-2659
promonocyte1.54e-2659
defensive cell2.43e-2648
phagocyte2.43e-2648
classical monocyte4.39e-2242
CD14-positive, CD16-negative classical monocyte4.39e-2242
leukocyte1.17e-21136
hematopoietic lineage restricted progenitor cell5.49e-21120
nongranular leukocyte3.89e-17115
stuff accumulating cell1.07e-1387
dendritic cell9.03e-0710
Uber Anatomy
Ontology termp-valuen
bone marrow8.28e-2876
hematopoietic system5.85e-2798
blood island5.85e-2798
bone element6.78e-2482
immune system3.62e-2393
skeletal element1.08e-2290
hemolymphoid system1.19e-22108
skeletal system1.02e-18100
adult organism6.00e-16114
neural tube2.16e-1456
neural rod2.16e-1456
future spinal cord2.16e-1456
neural keel2.16e-1456
regional part of nervous system7.24e-1353
regional part of brain7.24e-1353
regional part of forebrain5.36e-1141
forebrain5.36e-1141
anterior neural tube5.36e-1141
future forebrain5.36e-1141
brain grey matter4.43e-1034
gray matter4.43e-1034
telencephalon5.31e-1034
brain1.82e-0968
future brain1.82e-0968
regional part of telencephalon3.69e-0932
central nervous system3.78e-0981
cerebral hemisphere5.33e-0932
neural plate1.36e-0882
presumptive neural plate1.36e-0882
ecto-epithelium1.39e-07104
neurectoderm1.52e-0786
nervous system2.35e-0789
basal ganglion7.96e-079
nuclear complex of neuraxis7.96e-079
aggregate regional part of brain7.96e-079
collection of basal ganglia7.96e-079
cerebral subcortex7.96e-079
Disease
Ontology termp-valuen
leukemia3.20e-0839
myeloid leukemia3.85e-0831
hematologic cancer1.33e-0751
immune system cancer1.33e-0751


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
BATF#10538212.17890089615180.009566758805047810.0360246159307874
BCL11A#53335214.18472755180350.007108328585298740.0296290999808435
CHD2#110637.758017125587640.003351522464536340.0173042146862622
EBF1#187948.9064668465690.00015887907472010.00199893647568878
EP300#203335.08045629466740.01144298405398240.0419095880072193
GATA1#2623413.56030814380042.95627390049268e-050.000614795479676533
GATA2#2624412.7449317335543.78864877853583e-050.000722972208626903
IRF1#365935.727872815172930.008097114790333330.0320153922763543
JUNB#3726322.95797449486590.0001359772504018780.00177961504445135
MAFK#7975320.32554985337240.0001953213688931110.00235121812423094
MEF2A#4205418.74323090964418.0978922767748e-060.000224511752453964
MEF2C#4208441.31135449262413.42889182145094e-071.69881419801003e-05
NFKB1#479045.488063424193840.001102199566301980.00768698634424122
PAX5#507935.002174148383370.01196533174786410.0435129107007617
POU2F2#545249.106124057742520.000145395665174930.00188516174738727
REST#597837.237521537096020.004104697304192610.0195874294870041
SP1#666745.69838137814090.0009482606065333980.006851289483621
SPI1#668848.204323508522730.000220661881527680.0024968262453813
STAT2#6773348.94782838983051.42094046481278e-050.000340448729535631
STAT3#677437.889598747865680.003190760481680130.0167431961988741
TAF1#687243.343046285745290.008005664898701650.032284486692235
TAL1#6886322.40146250808020.0001462756395930170.00188930021314063
TBP#690843.706770687096390.005296377814784350.0244701792788437
TRIM28#10155418.59052504526258.36730015875654e-060.000230634062095639



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.