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MCL coexpression mm9:1037: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0.120671864823979,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.107511441879825,0,0,0,0.0572260417947564,0,0,0,0,0,0,0.127930999153497,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0.0978549673988937,1.17287026948828,0,0,0,0,0,0,0,0.873180132130182,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0,0,0,0,0.0189985734586218,0.00848956554074023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.15868109792089,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.456975733921281,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.25656024448328,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0978461107777356,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0865703124974023,0
|coexpression_dpi_cluster_scores_median=0.120671864823979,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.107511441879825,0,0,0,0.0572260417947564,0,0,0,0,0,0,0.127930999153497,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0509235292940968,0.0978549673988937,1.17287026948828,0,0,0,0,0,0,0,0.873180132130182,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0736278867910527,0,0,0,0,0,0,0,0,0,0,0,0.0189985734586218,0.00848956554074023,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.15868109792089,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.456975733921281,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.25656024448328,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0978461107777356,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0865703124974023,0
|gostat_on_MCL_coexpression=GO:0015125;bile acid transmembrane transporter activity;0.0315434894871784;108096!GO:0008028;monocarboxylic acid transmembrane transporter activity;0.0315434894871784;108096!
|gostat_on_MCL_coexpression=GO:0015125;bile acid transmembrane transporter activity;0.0315434894871784;108096!GO:0008028;monocarboxylic acid transmembrane transporter activity;0.0315434894871784;108096!
|ontology_enrichment_celltype=CL:0000197!6.40e-12!2;CL:0002491!6.40e-12!2;CL:0000098!6.40e-12!2;CL:0000006!6.09e-07!1;CL:0002374!6.09e-07!1;CL:0000202!6.09e-07!1;CL:0000199!6.09e-07!1;CL:0000855!6.09e-07!1;CL:0000589!6.09e-07!1
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000058!9.77e-20!7;UBERON:0000080!3.55e-13!4;UBERON:0005904!3.55e-13!4;UBERON:0006947!3.55e-13!4;UBERON:0002120!3.55e-13!4;UBERON:0004054!3.55e-13!4;UBERON:0004875!3.55e-13!4;UBERON:0004876!3.55e-13!4;UBERON:0005721!3.55e-13!4;UBERON:0005754!3.55e-13!4;UBERON:0007297!3.55e-13!4;UBERON:0010147!1.05e-12!2;UBERON:0003937!1.05e-12!2;UBERON:0005399!1.05e-12!2;UBERON:0004766!6.40e-12!2;UBERON:0008193!6.40e-12!2;UBERON:0005913!6.40e-12!2;UBERON:0011158!6.40e-12!2;UBERON:0005744!6.40e-12!2;UBERON:0003457!6.40e-12!2;UBERON:0008001!6.40e-12!2;UBERON:0007497!6.40e-12!2;UBERON:0009955!6.40e-12!2;UBERON:0003067!6.40e-12!2;UBERON:0002546!6.40e-12!2;UBERON:0007914!6.40e-12!2;UBERON:0005253!6.40e-12!2;UBERON:0002227!6.40e-12!2;UBERON:0001846!6.40e-12!2;UBERON:0004339!6.40e-12!2;UBERON:0002105!6.40e-12!2;UBERON:0001678!6.40e-12!2;UBERON:0003128!6.40e-12!2;UBERON:0001694!6.40e-12!2;UBERON:0004681!6.40e-12!2;UBERON:0001839!6.40e-12!2;UBERON:0001690!6.40e-12!2;UBERON:0001844!6.40e-12!2;UBERON:0001849!6.40e-12!2;UBERON:0002499!6.40e-12!2;UBERON:0001855!6.40e-12!2;UBERON:0011137!6.40e-12!2;UBERON:0001703!6.40e-12!2;UBERON:0010323!6.40e-12!2;UBERON:0003129!6.40e-12!2;UBERON:0003069!6.40e-12!2;UBERON:0003051!6.40e-12!2;UBERON:0004637!6.40e-12!2;UBERON:0004761!6.40e-12!2;UBERON:0010113!6.40e-12!2;UBERON:0009123!6.40e-12!2;UBERON:0010351!6.40e-12!2;UBERON:0009617!6.40e-12!2;UBERON:0005641!6.40e-12!2;UBERON:0010349!6.40e-12!2;UBERON:0000033!6.47e-11!13;UBERON:0001301!3.92e-08!3;UBERON:0006555!3.92e-08!3;UBERON:0005103!3.92e-08!3;UBERON:0000083!3.92e-08!3;UBERON:0009201!3.92e-08!3;UBERON:0004819!3.92e-08!3;UBERON:0006553!3.92e-08!3;UBERON:0003074!3.92e-08!3;UBERON:0003060!3.92e-08!3;UBERON:0000020!8.31e-08!12;UBERON:0001032!8.31e-08!12;UBERON:0004456!8.31e-08!12;UBERON:0000998!2.75e-07!1;UBERON:0007194!2.75e-07!1;UBERON:0006868!2.75e-07!1;UBERON:0005085!3.23e-07!13;UBERON:0001044!4.10e-07!1;UBERON:0001736!4.10e-07!1;UBERON:0003293!4.10e-07!1;UBERON:0003294!4.10e-07!1;UBERON:0001829!4.10e-07!1;UBERON:0010047!4.10e-07!1;UBERON:0000167!4.10e-07!1;UBERON:0006298!4.10e-07!1;UBERON:0002367!4.68e-07!1;UBERON:0009846!4.68e-07!1;UBERON:0003353!4.68e-07!1;UBERON:0004902!4.68e-07!1;UBERON:0003820!4.68e-07!1;UBERON:0009847!4.68e-07!1
}}
}}

Revision as of 16:13, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:69522935..69522942,+p@chr10:69522935..69522942
+
Mm9::chr2:105239751..105239799,-p5@Rcn1
Mm9::chr6:142271461..142271477,-p4@Slco1a5
Mm9::chr6:142271487..142271497,-p6@Slco1a5
Mm9::chr6:142271498..142271527,-p1@Slco1a5
Mm9::chr9:45197960..45197965,+p@chr9:45197960..45197965
+
Mm9::chr9:45197974..45197989,+p@chr9:45197974..45197989
+


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

GO IDGO nameFDR corrected p-value
GO:0015125bile acid transmembrane transporter activity0.0315434894871784
GO:0008028monocarboxylic acid transmembrane transporter activity0.0315434894871784



Relative expression of the co-expression cluster over median <br>Analyst:




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
duct9.77e-207
mesonephros3.55e-134
duct of male reproductive system3.55e-134
male genital duct3.55e-134
pronephros3.55e-134
internal male genitalia3.55e-134
nephrogenic cord3.55e-134
urogenital ridge3.55e-134
pronephric mesoderm3.55e-134
rostral part of nephrogenic cord3.55e-134
presumptive pronephric mesoderm3.55e-134
male accessory sex gland1.05e-122
sex gland1.05e-122
male reproductive gland1.05e-122
cranial bone6.40e-122
pneumatized bone6.40e-122
zone of bone organ6.40e-122
primary subdivision of skull6.40e-122
cranial conduit6.40e-122
head bone6.40e-122
irregular bone6.40e-122
developing epithelial placode6.40e-122
neurogenic placode6.40e-122
dorsolateral placode6.40e-122
cranial placode6.40e-122
head or neck bone6.40e-122
head mesenchyme6.40e-122
spiral organ of cochlea6.40e-122
internal ear6.40e-122
calvarium6.40e-122
vestibulo-auditory system6.40e-122
temporal bone6.40e-122
cranium6.40e-122
petrous part of temporal bone6.40e-122
vestibular system6.40e-122
bony labyrinth6.40e-122
ear6.40e-122
cochlea6.40e-122
membranous labyrinth6.40e-122
cochlear labyrinth6.40e-122
cochlear duct of membranous labyrinth6.40e-122
axial skeletal system6.40e-122
neurocranium6.40e-122
cranial skeletal system6.40e-122
skull6.40e-122
otic placode6.40e-122
ear vesicle6.40e-122
otic capsule6.40e-122
cartilaginous neurocranium6.40e-122
future membranous labyrinth6.40e-122
otic cup6.40e-122
otic capsule cartilage condensation6.40e-122
head paraxial mesoderm6.40e-122
otocyst epithelium6.40e-122
otic capsule pre-cartilage condensation6.40e-122
head6.47e-1113
epididymis3.92e-083
excretory tube3.92e-083
mesonephric epithelium3.92e-083
mesonephric tubule3.92e-083
nephric duct3.92e-083
kidney epithelium3.92e-083
renal duct3.92e-083
mesonephric duct3.92e-083
pronephric duct3.92e-083
sense organ8.31e-0812
sensory system8.31e-0812
entire sense organ system8.31e-0812
seminal vesicle2.75e-071
vesicular gland2.75e-071
seminal fluid secreting gland2.75e-071
ectodermal placode3.23e-0713
saliva-secreting gland4.10e-071
submandibular gland4.10e-071
gland of oral region4.10e-071
gland of foregut4.10e-071
major salivary gland4.10e-071
oral gland4.10e-071
oral cavity4.10e-071
submandibular gland primordium4.10e-071
prostate gland4.68e-071
embryonic cloacal epithelium4.68e-071
epithelium of hindgut4.68e-071
urogenital sinus epithelium4.68e-071
prostate bud4.68e-071
prostate field4.68e-071


TFBS overrepresentation<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}}}

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