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Coexpression cluster:C1215

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Full id: C1215_migratory_CD19_adult_immature_Dendritic_Burkitt_vein



Phase1 CAGE Peaks

Hg19::chr16:10972516..10972521,+p@chr16:10972516..10972521
+
Hg19::chr1:151319654..151319698,-p2@RFX5
Hg19::chr6:150954152..150954194,+p@chr6:150954152..150954194
+
Hg19::chr6:32977327..32977330,-p3@HLA-DOA
Hg19::chr6:32977332..32977343,-p2@HLA-DOA
Hg19::chr6:32977345..32977394,-p1@HLA-DOA
Hg19::chr6:33080222..33080247,+p1@HLA-DPB2


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
2.20729154564608e-050.0139721554839397278Antigen processing and presentation (KEGG):04612
0.0001207720034001940.03822433907616132182Tuberculosis (KEGG):05152



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:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.00128981675613196
GO:0042613MHC class II protein complex0.00128981675613196
GO:0042611MHC protein complex0.00609127997386628
GO:0019882antigen processing and presentation0.00609127997386628
GO:0032395MHC class II receptor activity0.0174762390536148
GO:0006955immune response0.0328749366611706
GO:0002376immune system process0.0381426036666276



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
leukocyte1.01e-46140
nongranular leukocyte1.73e-43119
hematopoietic lineage restricted progenitor cell2.13e-38124
hematopoietic stem cell9.09e-34172
angioblastic mesenchymal cell9.09e-34172
hematopoietic cell1.53e-33182
hematopoietic oligopotent progenitor cell1.40e-30165
hematopoietic multipotent progenitor cell1.40e-30165
lymphocyte9.65e-2553
common lymphoid progenitor9.65e-2553
lymphoid lineage restricted progenitor cell3.66e-2452
macrophage dendritic cell progenitor4.42e-1865
monopoietic cell5.97e-1763
monocyte5.97e-1763
monoblast5.97e-1763
promonocyte5.97e-1763
myeloid leukocyte4.57e-1676
lymphocyte of B lineage9.91e-1624
pro-B cell9.91e-1624
granulocyte monocyte progenitor cell1.36e-1571
CD14-positive, CD16-negative classical monocyte2.76e-1542
classical monocyte8.04e-1545
myeloid lineage restricted progenitor cell5.85e-1470
B cell1.41e-1014
myeloid cell4.53e-10112
common myeloid progenitor4.53e-10112
T cell4.90e-0925
pro-T cell4.90e-0925
dendritic cell4.18e-0810
mature alpha-beta T cell3.50e-0718
alpha-beta T cell3.50e-0718
immature T cell3.50e-0718
mature T cell3.50e-0718
immature alpha-beta T cell3.50e-0718
conventional dendritic cell7.02e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system7.02e-24102
blood island7.02e-24102
adult organism3.41e-23115
hemolymphoid system4.97e-22112
bone marrow6.88e-1480
immune system4.03e-12115
bone element9.39e-1286
blood3.86e-0915
haemolymphatic fluid3.86e-0915
organism substance3.86e-0915
skeletal element5.10e-08101
skeletal system5.10e-08101


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
NFKB1#479064.704054363594720.000216115061401970.00247758956067622
POU2F2#545256.504374326958950.0002767851340330550.00294850699849839
RFX5#599358.605650590853647.16524263203101e-050.00112751359838283
SRF#672235.913076398071920.01066868130167450.0393956230408933



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.