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Coexpression cluster:C4162: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4162_Small_Gingival_bone_Mammary_epidermoid_nasal_oral
|full_id=C4162_Small_Gingival_bone_Mammary_epidermoid_nasal_oral
|id=C4162
|id=C4162

Revision as of 17:12, 12 September 2012


Full id: C4162_Small_Gingival_bone_Mammary_epidermoid_nasal_oral



Phase1 CAGE Peaks

Hg19::chr2:192110104..192110170,+p1@MYO1B
Hg19::chr2:192110176..192110195,+p2@MYO1B
Hg19::chr2:192110199..192110210,+p3@MYO1B


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><br>

Uber Anatomy
Ontology termp-valuen
surface structure3.44e-2095
organism subdivision5.55e-19365
trunk1.40e-16216
skin of body1.10e-1340
mesenchyme1.10e-13238
entire embryonic mesenchyme1.10e-13238
trunk mesenchyme1.29e-13143
multi-tissue structure2.01e-13347
integument2.57e-1345
integumental system2.57e-1345
somite3.16e-1383
paraxial mesoderm3.16e-1383
presomitic mesoderm3.16e-1383
presumptive segmental plate3.16e-1383
trunk paraxial mesoderm3.16e-1383
presumptive paraxial mesoderm3.16e-1383
multilaminar epithelium1.59e-1282
cell layer9.25e-12312
epithelium1.50e-11309
unilaminar epithelium2.75e-11138
multi-cellular organism6.18e-11659
endoderm-derived structure1.57e-10169
endoderm1.57e-10169
presumptive endoderm1.57e-10169
dermomyotome3.30e-1070
anatomical system1.01e-09625
anatomical group1.94e-09626
digestive system2.48e-09155
digestive tract2.48e-09155
primitive gut2.48e-09155
skeletal muscle tissue1.69e-0861
striated muscle tissue1.69e-0861
myotome1.69e-0861
anatomical cluster3.83e-08286
muscle tissue5.16e-0863
musculature5.16e-0863
musculature of body5.16e-0863
primordium2.82e-07168
vasculature5.36e-0779
vascular system5.36e-0779
mouth5.75e-0728
stomodeum5.75e-0728
epithelial tube8.63e-07118
endo-epithelium9.38e-0782


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-050.000285007250486415
CTCF#1066435.360256373075030.0064925092527670.0280148394418168
E2F1#186934.907389214879320.008460985347239390.0326193004311678
E2F6#187635.017155731697390.00791769806886330.0323089969764013
FOXA1#3169311.08141974938550.000734755275698670.00582356425883686
HDAC2#3066313.41562023662630.0004140761399857210.003920734178057
MYC#460935.22228187160940.007020843755740150.0295153524536387
RAD21#5885310.35503389545630.0009004912073565420.00665626733704507
SIN3A#2594235.408884726815140.006318961977991520.0277428144450755
SMARCB1#6598212.16847718743830.008675002221921740.0329973615855805
SMC3#9126315.04493284493280.0002935825420371870.00309743076147305
TAF7#6879311.43306940492390.0006690181981945830.00544256049238542
TCF7L2#6934310.77017656313730.0008003181298398380.00614998345687167
TFAP2C#7022310.80922860986020.0007916746575753130.00616981639896337
ZNF263#1012738.221841637010680.001799043925565870.0109646561941045



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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