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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
leukocyte3.58e-52136
hematopoietic cell2.36e-45177
hematopoietic stem cell8.71e-45168
angioblastic mesenchymal cell8.71e-45168
nongranular leukocyte1.39e-42115
hematopoietic oligopotent progenitor cell2.79e-42161
hematopoietic multipotent progenitor cell2.79e-42161
hematopoietic lineage restricted progenitor cell3.72e-40120
myeloid leukocyte1.34e-3272
granulocyte monocyte progenitor cell3.44e-2967
macrophage dendritic cell progenitor2.19e-2861
defensive cell2.30e-2748
phagocyte2.30e-2748
monopoietic cell4.37e-2759
monocyte4.37e-2759
monoblast4.37e-2759
promonocyte4.37e-2759
myeloid cell9.49e-27108
common myeloid progenitor9.49e-27108
myeloid lineage restricted progenitor cell3.83e-2566
classical monocyte5.13e-2542
CD14-positive, CD16-negative classical monocyte5.13e-2542
lymphocyte7.28e-1453
common lymphoid progenitor7.28e-1453
lymphoid lineage restricted progenitor cell1.99e-1352
nucleate cell2.67e-1255
stuff accumulating cell7.30e-1187
mesenchymal cell8.90e-11354
connective tissue cell1.62e-10361
lymphocyte of B lineage3.14e-1024
pro-B cell3.14e-1024
dendritic cell2.18e-0710
stem cell4.91e-07441
Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.13e-34108
hematopoietic system1.16e-3398
blood island1.16e-3398
immune system2.55e-2893
bone marrow2.58e-2576
bone element1.12e-2282
skeletal element3.53e-2090
skeletal system2.78e-16100
lateral plate mesoderm1.31e-15203
connective tissue9.21e-10371
blood4.04e-0715
haemolymphatic fluid4.04e-0715
organism substance4.04e-0715


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.