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Coexpression cluster:C1035: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1035_CD8_Eosinophils_Natural_Basophils_CD4_Peripheral_CD19
|full_id=C1035_CD8_Eosinophils_Natural_Basophils_CD4_Peripheral_CD19
|id=C1035
|id=C1035

Revision as of 13:27, 12 September 2012


Full id: C1035_CD8_Eosinophils_Natural_Basophils_CD4_Peripheral_CD19



Phase1 CAGE Peaks

Hg19::chr14:64971438..64971450,+p2@ZBTB1
Hg19::chr14:64971461..64971542,+p1@ZBTB1
Hg19::chr16:85833774..85833799,-p@chr16:85833774..85833799
-
Hg19::chr21:38739399..38739420,+p6@DYRK1A
Hg19::chr2:109336045..109336054,+p6@RANBP2
Hg19::chr3:150126440..150126455,+p9@TSC22D2
Hg19::chr7:104654690..104654704,+p2@MLL5
Hg19::chr7:104654718..104654741,+p3@MLL5


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><br>


Cell Type
Ontology termp-valuen
leukocyte7.01e-46140
hematopoietic stem cell4.12e-38172
angioblastic mesenchymal cell4.12e-38172
hematopoietic lineage restricted progenitor cell1.65e-35124
hematopoietic cell1.79e-34182
hematopoietic oligopotent progenitor cell4.99e-34165
hematopoietic multipotent progenitor cell4.99e-34165
nongranular leukocyte1.18e-33119
myeloid leukocyte3.13e-2576
CD14-positive, CD16-negative classical monocyte6.27e-2342
granulocyte monocyte progenitor cell4.12e-2271
myeloid lineage restricted progenitor cell3.21e-2070
classical monocyte5.03e-2045
myeloid cell1.76e-19112
common myeloid progenitor1.76e-19112
macrophage dendritic cell progenitor4.61e-1965
monopoietic cell6.07e-1863
monocyte6.07e-1863
monoblast6.07e-1863
promonocyte6.07e-1863
mesenchymal cell8.81e-14358
lymphocyte1.15e-1353
common lymphoid progenitor1.15e-1353
lymphoid lineage restricted progenitor cell1.21e-1352
connective tissue cell2.66e-12365
multi fate stem cell1.93e-11430
somatic stem cell5.22e-11436
stem cell5.37e-11444
motile cell2.69e-10390
mature alpha-beta T cell9.67e-1018
alpha-beta T cell9.67e-1018
immature T cell9.67e-1018
mature T cell9.67e-1018
immature alpha-beta T cell9.67e-1018
T cell6.27e-0925
pro-T cell6.27e-0925
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.23e-23102
blood island1.23e-23102
hemolymphoid system7.14e-23112
bone element1.84e-1986
bone marrow7.29e-1980
skeletal element1.02e-15101
skeletal system1.02e-15101
immune system9.41e-13115
connective tissue1.76e-12375


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#90575.54417637984231.68072647241023e-050.00038706370904532
CEBPB#105143.985573812912410.01139163688734390.0417434884697838
E2F1#186984.907389214879322.97124777369457e-060.000101509370702286
E2F6#187663.762866798773040.001207680027997810.00818593551687848
ELF1#199773.72583571395660.0002503412725512720.0026987399013194
FOXA1#316945.540709874692730.003444272925946160.017521501223229
FOXA2#317039.236423907249470.003211939548395410.0168433297095234
GABPB1#255354.417302397613860.002182228654850360.012587527807573
GTF2F1#296246.369830438378830.002051908375195520.01191147011267
HEY1#2346273.53509716271750.0003566123056684080.00356745522909031
HMGN3#932455.111592327094120.001109515975889930.00770815798616164
JUND#372754.371664963669390.002289022009366710.0129897397107286
MYC#460963.916711403707050.0009649270569246440.00693906334078034
NFKB1#479064.116047568145380.0007299856589784310.00581532969016387
NR3C1#290835.614883749189890.01292443946090990.0464636512635701
PAX5#507965.002174148383370.0002416084515475770.00262929509963295
POLR2A#543082.147453176558070.002210725788971910.0127181883152163
POU2F2#545255.691327536089080.000670954773528490.00541528945846538
SIN3A#2594253.380552954259460.007342226961170280.0303640944641507
SIX5#14791236.407518258297120.008979882420728990.0340491555379943
SMARCB1#659836.844768417934030.007473690134633950.0308235487095145
SPI1#668844.102161754261360.01027800662400760.0381892960653455
TAF1#687272.925165500027130.001265325357915740.00849070387145734
TBP#690873.243424351209340.0006354223620492050.0052122899835106
TCF12#693856.646540563866510.0003223768920812840.0032995609792314
YY1#752853.069481718658660.0112591365358360.0413290088804365
ZNF263#1012766.166381227758017.27120729623729e-050.00114263860790209



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.