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Coexpression cluster:C2451: Difference between revisions

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}}
}}

Revision as of 15:30, 26 November 2012


Full id: C2451_salivary_esophagus_tonsil_tongue_trachea_throat_cervix



Phase1 CAGE Peaks

Hg19::chr17:995098..995115,-p34@ABR
Hg19::chr17:995135..995149,-p25@ABR
Hg19::chr17:995247..995256,-p45@ABR
Hg19::chr2:62668844..62668859,+p@chr2:62668844..62668859
+


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
saliva-secreting gland2.41e-356
gland of oral region2.41e-356
gland of foregut2.41e-356
oral gland2.41e-356
oral cavity2.41e-356
gland of gut5.23e-2110
oral opening1.66e-2022
orifice9.33e-1836
respiratory system1.30e-1674
foregut1.06e-1587
mouth3.48e-1529
stomodeum3.48e-1529
subdivision of digestive tract1.60e-13118
major salivary gland1.14e-122
open tracheal system trachea1.21e-122
endoderm-derived structure2.24e-11160
endoderm2.24e-11160
presumptive endoderm2.24e-11160
exocrine gland6.82e-1131
exocrine system6.82e-1131
anatomical space1.33e-1095
subdivision of head2.70e-1049
digestive system2.79e-10145
digestive tract2.79e-10145
primitive gut2.79e-10145
adult organism8.15e-10114
thoracic cavity element1.52e-0934
thoracic cavity1.52e-0934
anterior region of body1.73e-0962
craniocervical region1.73e-0962
tracheobronchial tree2.95e-0915
lower respiratory tract2.95e-0915
thoracic segment organ3.07e-0935
esophagus6.92e-093
tongue6.92e-093
gustatory system6.92e-093
esophageal region6.92e-093
future tongue6.92e-093
respiratory tract8.71e-0954
head8.75e-0956
male genital duct9.45e-093
internal male genitalia9.45e-093
lower respiratory tract epithelium2.19e-083
epithelium of bronchus2.19e-083
gland4.76e-0859
immaterial anatomical entity4.87e-08117
trachea6.83e-087
respiratory airway6.83e-087
organism subdivision1.11e-07264
tonsil1.65e-071
mucosa-associated lymphoid tissue1.65e-071
lymphoid tissue1.65e-071
tonsillar ring1.65e-071
thoracic segment of trunk2.08e-0752
epididymis2.23e-071
penis2.67e-071
intromittent organ2.67e-071
lateral plate mesenchyme2.67e-071
undifferentiated genital tubercle2.67e-071
somatopleure2.67e-071
submandibular gland2.84e-071
submandibular gland primordium2.84e-071
parotid gland4.57e-071
cheek4.57e-071
parotid gland primordium4.57e-071
vas deferens5.45e-071
spermatic cord5.45e-071
duct of male reproductive system9.21e-074


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

No analysis results for this cluster

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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