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Coexpression cluster:C2054

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Full id: C2054_Eosinophils_Dendritic_Neutrophils_CD19_CD14_Basophils_CD34



Phase1 CAGE Peaks

Hg19::chr10:30723045..30723060,+p2@MAP3K8
Hg19::chr15:75495066..75495090,-p@chr15:75495066..75495090
-
Hg19::chr19:45504688..45504782,+p1@RELB
Hg19::chr6:44233297..44233330,-p2@NFKBIE


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


p.valueFDRnGenesnPathwayName
0.0002618095438293840.03314508824882268MAPK signaling pathway (KEGG):04010
4.24401547463794e-050.008954872651486052108T cell receptor signaling pathway (KEGG):04660
2.8113975272981e-070.000177961463477973188TNF-alpha/NF-kB Signaling Pathway (Wikipathways):WP231
6.25100917324437e-050.009892222016659212131IL-5 up reg. targets (Netpath):NetPath_17
3.88503833680646e-060.00122961463359924233{NFKB1,33} (Static Module):NA



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:0043011myeloid dendritic cell differentiation0.0085925308502013
GO:0001773myeloid dendritic cell activation0.0085925308502013
GO:0045063T-helper 1 cell differentiation0.0085925308502013
GO:0042994cytoplasmic sequestering of transcription factor0.0085925308502013
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0085925308502013
GO:0002292T cell differentiation during immune response0.0085925308502013
GO:0042093T-helper cell differentiation0.0085925308502013
GO:0002366leukocyte activation during immune response0.0085925308502013
GO:0002285lymphocyte activation during immune response0.0085925308502013
GO:0051220cytoplasmic sequestering of protein0.0085925308502013
GO:0002293alpha-beta T cell differentiation during immune response0.0085925308502013
GO:0002286T cell activation during immune response0.0085925308502013
GO:0002263cell activation during immune response0.0085925308502013
GO:0042308negative regulation of protein import into nucleus0.0085925308502013
GO:0042992negative regulation of transcription factor import into nucleus0.0085925308502013
GO:0043367CD4-positive, alpha beta T cell differentiation0.0085925308502013
GO:0042088T-helper 1 type immune response0.0085925308502013
GO:0046823negative regulation of nucleocytoplasmic transport0.0085925308502013
GO:0051224negative regulation of protein transport0.00881839046160363
GO:0046632alpha-beta T cell differentiation0.0103098228262197
GO:0004709MAP kinase kinase kinase activity0.0109026941205202
GO:0046631alpha-beta T cell activation0.0109026941205202
GO:0042990regulation of transcription factor import into nucleus0.0109026941205202
GO:0042991transcription factor import into nucleus0.0109026941205202
GO:0042306regulation of protein import into nucleus0.0109026941205202
GO:0033157regulation of intracellular protein transport0.0109026941205202
GO:0032507maintenance of cellular protein localization0.0111067793515641
GO:0051651maintenance of cellular localization0.0111067793515641
GO:0032386regulation of intracellular transport0.0111067793515641
GO:0045185maintenance of protein localization0.0111656867381263
GO:0002274myeloid leukocyte activation0.0112207691804314
GO:0051223regulation of protein transport0.0112723852677017
GO:0046822regulation of nucleocytoplasmic transport0.0113208501237992
GO:0002573myeloid leukocyte differentiation0.0113664417991907
GO:0051051negative regulation of transport0.0114094065671464
GO:0030217T cell differentiation0.0142699894330178
GO:0051235maintenance of localization0.0142699894330178
GO:0030098lymphocyte differentiation0.0216742314407406
GO:0002250adaptive immune response0.0235842708301034
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.0235842708301034
GO:0030099myeloid cell differentiation0.0235842708301034
GO:0004702receptor signaling protein serine/threonine kinase activity0.0235842708301034
GO:0002521leukocyte differentiation0.0269146502620051
GO:0006606protein import into nucleus0.0273892766352992
GO:0051170nuclear import0.0273892766352992
GO:0042110T cell activation0.0273892766352992
GO:0003714transcription corepressor activity0.0292605890034004
GO:0051049regulation of transport0.0294516884986195
GO:0017038protein import0.0319866615733457
GO:0006913nucleocytoplasmic transport0.0385026978699054
GO:0046649lymphocyte activation0.0385026978699054
GO:0051169nuclear transport0.0385026978699054
GO:0030097hemopoiesis0.0389812617561175
GO:0048534hemopoietic or lymphoid organ development0.0409480756328063
GO:0005057receptor signaling protein activity0.0409480756328063
GO:0045321leukocyte activation0.0409480756328063
GO:0002520immune system development0.0409480756328063
GO:0001775cell activation0.0461752674458715
GO:0016564transcription repressor activity0.0464717294069291
GO:0006605protein targeting0.0465458612671562



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
leukocyte1.66e-49140
hematopoietic stem cell6.29e-40172
angioblastic mesenchymal cell6.29e-40172
hematopoietic cell2.24e-39182
nongranular leukocyte9.40e-39119
hematopoietic lineage restricted progenitor cell9.26e-38124
hematopoietic oligopotent progenitor cell2.66e-37165
hematopoietic multipotent progenitor cell2.66e-37165
myeloid leukocyte6.88e-3076
granulocyte monocyte progenitor cell1.75e-2671
CD14-positive, CD16-negative classical monocyte1.58e-2542
macrophage dendritic cell progenitor3.45e-2465
monopoietic cell5.06e-2363
monocyte5.06e-2363
monoblast5.06e-2363
promonocyte5.06e-2363
myeloid lineage restricted progenitor cell9.23e-2370
myeloid cell2.62e-22112
common myeloid progenitor2.62e-22112
classical monocyte8.93e-2245
lymphocyte9.97e-1453
common lymphoid progenitor9.97e-1453
lymphoid lineage restricted progenitor cell2.41e-1352
lymphocyte of B lineage2.47e-1024
pro-B cell2.47e-1024
mesenchymal cell3.70e-09358
connective tissue cell6.13e-09365
dendritic cell5.08e-0710
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.29e-32112
hematopoietic system1.61e-31102
blood island1.61e-31102
immune system4.66e-23115
bone marrow5.78e-2380
bone element6.81e-2086
lateral plate mesoderm9.24e-19216
skeletal element1.01e-14101
skeletal system1.01e-14101
connective tissue3.38e-08375
blood1.79e-0715
haemolymphatic fluid1.79e-0715
organism substance1.79e-0715
musculoskeletal system3.46e-07167


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#90546.336201576962630.0006203100587215640.00511080484559967
NFKB1#479045.488063424193840.001102199566301980.00766293572793318
PAX5#507946.669565531177830.0005052774169483260.0044292989884729
SIN3A#2594245.408884726815140.001168172384885160.0079392695845006
TAF1#687243.343046285745290.008005664898701650.0321072015804117
ZBTB7A#5134135.513931980906920.009038352821081090.0342174404712686



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.