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Coexpression cluster:C2739: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.37e-51!115;UBERON:0001049!3.10e-34!57;UBERON:0005068!3.10e-34!57;UBERON:0006241!3.10e-34!57;UBERON:0007135!3.10e-34!57;UBERON:0005743!4.90e-33!86;UBERON:0001017!1.53e-32!82;UBERON:0000073!4.05e-32!94;UBERON:0001016!4.05e-32!94;UBERON:0003075!1.67e-27!86;UBERON:0007284!1.67e-27!86;UBERON:0002616!2.40e-27!59;UBERON:0000955!1.35e-26!69;UBERON:0006238!1.35e-26!69;UBERON:0003080!5.33e-26!42;UBERON:0002780!1.58e-25!41;UBERON:0001890!1.58e-25!41;UBERON:0006240!1.58e-25!41;UBERON:0002346!5.89e-25!90;UBERON:0000025!5.95e-24!194;UBERON:0004111!4.70e-23!241;UBERON:0002020!1.28e-21!34;UBERON:0003528!1.28e-21!34;UBERON:0001893!1.64e-21!34;UBERON:0002791!9.50e-21!33;UBERON:0000477!1.00e-20!286;UBERON:0001869!3.00e-20!32;UBERON:0003056!2.58e-18!61;UBERON:0002619!1.35e-17!22;UBERON:0001950!2.52e-16!20;UBERON:0000956!4.19e-16!25;UBERON:0000203!4.19e-16!25;UBERON:0000153!2.21e-15!129;UBERON:0007811!2.21e-15!129;UBERON:0000033!7.48e-15!123;UBERON:0004121!1.43e-14!169;UBERON:0000483!7.03e-14!309;UBERON:0000924!1.66e-13!173;UBERON:0006601!1.66e-13!173;UBERON:0000119!2.64e-13!312;UBERON:0000467!3.67e-11!625;UBERON:0000480!5.08e-11!626;UBERON:0000468!9.12e-11!659;UBERON:0003076!2.84e-09!15;UBERON:0003057!2.84e-09!15;UBERON:0001986!1.94e-08!18;UBERON:0004638!1.94e-08!18;UBERON:0004852!1.94e-08!18;UBERON:0004732!4.52e-08!13;UBERON:0000481!1.05e-07!347;UBERON:0000922!1.19e-07!612;UBERON:0004733!2.33e-07!12;UBERON:0002028!2.33e-07!12;UBERON:0007277!2.33e-07!12;UBERON:0002298!2.69e-07!8;UBERON:0000064!3.41e-07!219;UBERON:0001871!4.49e-07!7;UBERON:0002308!5.65e-07!9;UBERON:0000125!5.65e-07!9;UBERON:0002420!9.44e-07!9;UBERON:0007245!9.44e-07!9;UBERON:0010009!9.44e-07!9;UBERON:0010011!9.44e-07!9;UBERON:0000454!9.44e-07!9
|ontology_enrichment_uberon=UBERON:0007023!1.37e-51!115;UBERON:0001049!3.10e-34!57;UBERON:0005068!3.10e-34!57;UBERON:0006241!3.10e-34!57;UBERON:0007135!3.10e-34!57;UBERON:0005743!4.90e-33!86;UBERON:0001017!1.53e-32!82;UBERON:0000073!4.05e-32!94;UBERON:0001016!4.05e-32!94;UBERON:0003075!1.67e-27!86;UBERON:0007284!1.67e-27!86;UBERON:0002616!2.40e-27!59;UBERON:0000955!1.35e-26!69;UBERON:0006238!1.35e-26!69;UBERON:0003080!5.33e-26!42;UBERON:0002780!1.58e-25!41;UBERON:0001890!1.58e-25!41;UBERON:0006240!1.58e-25!41;UBERON:0002346!5.89e-25!90;UBERON:0000025!5.95e-24!194;UBERON:0004111!4.70e-23!241;UBERON:0002020!1.28e-21!34;UBERON:0003528!1.28e-21!34;UBERON:0001893!1.64e-21!34;UBERON:0002791!9.50e-21!33;UBERON:0000477!1.00e-20!286;UBERON:0001869!3.00e-20!32;UBERON:0003056!2.58e-18!61;UBERON:0002619!1.35e-17!22;UBERON:0001950!2.52e-16!20;UBERON:0000956!4.19e-16!25;UBERON:0000203!4.19e-16!25;UBERON:0000153!2.21e-15!129;UBERON:0007811!2.21e-15!129;UBERON:0000033!7.48e-15!123;UBERON:0004121!1.43e-14!169;UBERON:0000483!7.03e-14!309;UBERON:0000924!1.66e-13!173;UBERON:0006601!1.66e-13!173;UBERON:0000119!2.64e-13!312;UBERON:0000467!3.67e-11!625;UBERON:0000480!5.08e-11!626;UBERON:0000468!9.12e-11!659;UBERON:0003076!2.84e-09!15;UBERON:0003057!2.84e-09!15;UBERON:0001986!1.94e-08!18;UBERON:0004638!1.94e-08!18;UBERON:0004852!1.94e-08!18;UBERON:0004732!4.52e-08!13;UBERON:0000481!1.05e-07!347;UBERON:0000922!1.19e-07!612;UBERON:0004733!2.33e-07!12;UBERON:0002028!2.33e-07!12;UBERON:0007277!2.33e-07!12;UBERON:0002298!2.69e-07!8;UBERON:0000064!3.41e-07!219;UBERON:0001871!4.49e-07!7;UBERON:0002308!5.65e-07!9;UBERON:0000125!5.65e-07!9;UBERON:0002420!9.44e-07!9;UBERON:0007245!9.44e-07!9;UBERON:0010009!9.44e-07!9;UBERON:0010011!9.44e-07!9;UBERON:0000454!9.44e-07!9
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}}
}}

Revision as of 14:21, 5 September 2012


Full id: C2739_retina_cerebellum_Hepatocyte_salivary_submaxillary_parotid_small



Phase1 CAGE Peaks

Hg19::chr3:39851061..39851085,+p4@MYRIP
Hg19::chr3:39851094..39851151,+p1@MYRIP
Hg19::chr3:39851154..39851165,+p6@MYRIP
Hg19::chr3:39851170..39851195,+p3@MYRIP


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
adult organism1.37e-51115
neural tube3.10e-3457
neural rod3.10e-3457
future spinal cord3.10e-3457
neural keel3.10e-3457
central nervous system1.53e-3282
regional part of nervous system4.05e-3294
nervous system4.05e-3294
neural plate1.67e-2786
presumptive neural plate1.67e-2786
regional part of brain2.40e-2759
brain1.35e-2669
future brain1.35e-2669
anterior neural tube5.33e-2642
regional part of forebrain1.58e-2541
forebrain1.58e-2541
future forebrain1.58e-2541
neurectoderm5.89e-2590
tube5.95e-24194
anatomical conduit4.70e-23241
gray matter1.28e-2134
brain grey matter1.28e-2134
telencephalon1.64e-2134
regional part of telencephalon9.50e-2133
anatomical cluster1.00e-20286
cerebral hemisphere3.00e-2032
pre-chordal neural plate2.58e-1861
regional part of cerebral cortex1.35e-1722
neocortex2.52e-1620
cerebral cortex4.19e-1625
pallium4.19e-1625
anterior region of body2.21e-15129
craniocervical region2.21e-15129
head7.48e-15123
ectoderm-derived structure1.43e-14169
epithelium7.03e-14309
ectoderm1.66e-13173
presumptive ectoderm1.66e-13173
cell layer2.64e-13312
anatomical system3.67e-11625
anatomical group5.08e-11626
multi-cellular organism9.12e-11659
posterior neural tube2.84e-0915
chordal neural plate2.84e-0915
endothelium1.94e-0818
blood vessel endothelium1.94e-0818
cardiovascular system endothelium1.94e-0818
segmental subdivision of nervous system4.52e-0813
multi-tissue structure1.05e-07347
embryo1.19e-07612
segmental subdivision of hindbrain2.33e-0712
hindbrain2.33e-0712
presumptive hindbrain2.33e-0712
brainstem2.69e-078
organ part3.41e-07219
temporal lobe4.49e-077
nucleus of brain5.65e-079
neural nucleus5.65e-079
basal ganglion9.44e-079
nuclear complex of neuraxis9.44e-079
aggregate regional part of brain9.44e-079
collection of basal ganglia9.44e-079
cerebral subcortex9.44e-079


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
CCNT2#90546.336201576962630.0006203100587215640.00513104405376378
CTCF#1066445.360256373075030.001211145381643620.00818763755022838
E2F1#186944.907389214879320.001724022357361790.0106667755320206
E2F6#187645.017155731697390.00157802193473060.00998285982441874
EGR1#195844.988179094810140.001615011500076050.0101584067728525
NFYA#4800418.42558069983058.67100748407158e-060.000234852528690081
NFYB#4801416.75979325353651.26678572070404e-050.000311665097490246
RAD21#5885410.35503389545638.6948481184721e-050.00129725891806444



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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