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Coexpression cluster:C4373

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Full id: C4373_Hepatocyte_small_hepatocellular_Endothelial_liver_Renal_duodenum



Phase1 CAGE Peaks

Hg19::chr4:140587092..140587103,+p7@MGST2
Hg19::chr4:140587108..140587121,+p5@MGST2
Hg19::chr4:140587123..140587175,+p3@MGST2


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>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia2.53e-0831


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285429796447107
EBF1#187938.9064668465690.00141523283560980.0091793256811733
ELF1#199734.258097958807540.01295179875054610.0464102418756702
EP300#203336.77394172622320.003216880500103790.0168042706222348
FOS#235338.99795530889440.001372499272417130.00900335729614802
FOSL2#2355316.93020060456170.0002060162053171620.00243725945481639
FOXA1#3169311.08141974938550.000734755275698670.00583153022560174
FOXA2#3170324.63046375266526.68983856509345e-050.00107555426400831
GABPB1#255337.067683836182170.002832212825417420.0154598586355391
GATA1#2623313.56030814380040.0004009615963782630.00388893277898862
GATA2#2624312.7449317335540.0004829527704283790.00438181777350096
GTF2F1#2962312.73966087675770.0004835525047438590.00435247264008825
HDAC2#3066313.41562023662630.0004140761399857210.00392749958986184
HNF4A#3172323.13229036295378.07584663437677e-050.00123254909637246
HNF4G#3174328.75342252644684.20470658818262e-050.000759224328082996
RXRA#6256320.07461713913330.0001235730348432220.00165757053506182
SIN3A#2594235.408884726815140.006318961977991520.0277731701885134
SP1#666735.69838137814090.005403962701712170.0247461069234935
SRF#6722313.79717826216780.0003806615025800190.00375942379838814
TCF12#6938310.63446490218640.0008313523990202070.00630862553231645
TCF7L2#6934310.77017656313730.0008003181298398380.00616177111406877
TFAP2A#7020316.5186343730450.0002218033880766340.00249058424334325
TFAP2C#7022310.80922860986020.0007916746575753130.00617765313527407
YY1#752834.911170749853860.008441455341808260.0330589903420996



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.

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