Personal tools

Coexpression cluster:C2428

From FANTOM5_SSTAR

Revision as of 14:00, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2428_Mast_CD14_Eosinophils_immature_CD19_CD4_CD8



Phase1 CAGE Peaks

Hg19::chr17:62502942..62502965,-p6@DDX5
Hg19::chr2:157189180..157189290,-p1@NR4A2
Hg19::chr2:157189298..157189305,-p23@NR4A2
Hg19::chr9:102584128..102584144,+p3@NR4A3


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


GO IDGO nameFDR corrected p-value
GO:0003707steroid hormone receptor activity0.00364664345425225
GO:0004879ligand-dependent nuclear receptor activity0.00364664345425225
GO:0042053regulation of dopamine metabolic process0.0106843266182394
GO:0042069regulation of catecholamine metabolic process0.0106843266182394
GO:0004887thyroid hormone receptor activity0.0195838960000424
GO:0042417dopamine metabolic process0.0195838960000424
GO:0016070RNA metabolic process0.0284680595302614
GO:0043565sequence-specific DNA binding0.0284680595302614
GO:0006584catecholamine metabolic process0.0284680595302614
GO:0018958phenol metabolic process0.0284680595302614
GO:0003724RNA helicase activity0.0284680595302614
GO:0042133neurotransmitter metabolic process0.0284680595302614
GO:0010467gene expression0.038496700016013
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0428660141712666
GO:0003700transcription factor activity0.0428660141712666
GO:0005634nucleus0.0428660141712666
GO:0006576biogenic amine metabolic process0.0437664922796501
GO:0003676nucleic acid binding0.0437664922796501
GO:0001505regulation of neurotransmitter levels0.0437664922796501
GO:0065007biological regulation0.0456741439377732
GO:0006575amino acid derivative metabolic process0.0456741439377732



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
myeloid leukocyte5.32e-2572
classical monocyte1.13e-2442
CD14-positive, CD16-negative classical monocyte1.13e-2442
leukocyte2.92e-24136
defensive cell1.55e-2248
phagocyte1.55e-2248
granulocyte monocyte progenitor cell6.83e-2267
macrophage dendritic cell progenitor1.46e-1961
myeloid lineage restricted progenitor cell8.04e-1966
hematopoietic stem cell2.36e-18168
angioblastic mesenchymal cell2.36e-18168
monopoietic cell2.41e-1859
monocyte2.41e-1859
monoblast2.41e-1859
promonocyte2.41e-1859
hematopoietic lineage restricted progenitor cell1.12e-17120
nongranular leukocyte9.99e-17115
myeloid cell1.86e-16108
common myeloid progenitor1.86e-16108
hematopoietic oligopotent progenitor cell3.47e-16161
hematopoietic multipotent progenitor cell3.47e-16161
hematopoietic cell8.28e-16177
stuff accumulating cell5.49e-0887
Uber Anatomy
Ontology termp-valuen
bone marrow1.54e-1776
bone element3.44e-1782
hematopoietic system1.14e-1598
blood island1.14e-1598
skeletal element9.33e-1490
skeletal system6.82e-13100
immune system1.55e-1293
hemolymphoid system1.10e-11108
adult organism8.80e-11114


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
BRCA1#672315.13817298241780.0004682184421431190.00430119323414418
CCNT2#90546.336201576962630.0006203100587215640.00512049970145601
CTBP2#1488231.35850016966410.001492676882047230.00954003309981829
E2F1#186944.907389214879320.001724022357361790.010647851625104
E2F4#187439.501045236463330.001850751034728270.0109271630570403
E2F6#187645.017155731697390.00157802193473060.0099665597993063
ELF1#199744.258097958807540.003041525565781240.0160845556010242
ELK4#2005312.1767612438510.0008912632577620610.00663738187231973
ETS1#211337.296570691651750.00400857377511390.0192041943348221
FOXA1#3169411.08141974938556.62943068949433e-050.00107029078958123
GABPB1#255335.300762877136630.01012678824234270.0378577383842944
HEY1#2346244.040111043105710.00375304636917980.0185959014019722
IRF1#365947.63716375356390.0002938853996185490.00307392060598514
MAX#414934.839416631755340.01315737137836840.0466190361441652
MYC#460945.22228187160940.001344309395272740.00887417539554322
NFYA#4800313.81918552487290.0006132411806734510.00508707670121959
NFYB#4801312.56984494015230.000811456397697350.0061886734861336
RFX5#599339.035933120396320.002144561191324070.0123846185380533
SETDB1#9869220.16001308900520.00356908685407640.0180842160854301
SIN3A#2594245.408884726815140.001168172384885160.00795946997031712
SP1#666745.69838137814090.0009482606065333980.00683851605342781
TAF1#687243.343046285745290.008005664898701650.0322061413795887
TBP#690843.706770687096390.005296377814784350.024408631303427
TCF7L2#6934410.77017656313737.42969445082454e-050.00115400038481509
USF1#739146.361499277207960.0006105011399140830.00507846503795197
YY1#752844.911170749853860.00171871838055440.0106814179676716



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.