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Coexpression cluster:C2911: Difference between revisions

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}}
}}

Revision as of 15:48, 26 November 2012


Full id: C2911_Monocytederived_Macrophage_corpus_spinal_CD14_diencephalon_insula



Phase1 CAGE Peaks

Hg19::chr7:99764744..99764756,-p7@GAL3ST4
Hg19::chr7:99764761..99764795,-p4@GAL3ST4
Hg19::chr7:99764796..99764842,-p2@GAL3ST4
Hg19::chr7:99764857..99764886,-p3@GAL3ST4


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>


Cell Type
Ontology termp-valuen
macrophage2.01e-106
Uber Anatomy
Ontology termp-valuen
adult organism6.93e-72114
neural tube9.69e-4756
neural rod9.69e-4756
future spinal cord9.69e-4756
neural keel9.69e-4756
regional part of nervous system2.17e-4253
regional part of brain2.17e-4253
central nervous system5.76e-3781
regional part of forebrain8.90e-3741
forebrain8.90e-3741
anterior neural tube8.90e-3741
future forebrain8.90e-3741
neural plate3.31e-3382
presumptive neural plate3.31e-3382
brain4.42e-3368
future brain4.42e-3368
nervous system1.18e-3189
neurectoderm6.42e-3186
telencephalon1.12e-2934
brain grey matter2.72e-2934
gray matter2.72e-2934
regional part of telencephalon8.70e-2732
cerebral hemisphere1.06e-2632
pre-chordal neural plate4.79e-2461
ecto-epithelium7.43e-23104
organ system subdivision6.66e-22223
regional part of cerebral cortex1.99e-2122
structure with developmental contribution from neural crest4.43e-21132
neocortex1.22e-1820
cerebral cortex3.16e-1825
pallium3.16e-1825
organ1.27e-15503
ectoderm-derived structure1.58e-15171
ectoderm1.58e-15171
presumptive ectoderm1.58e-15171
basal ganglion3.30e-139
neural nucleus3.30e-139
nuclear complex of neuraxis3.30e-139
nucleus of brain3.30e-139
aggregate regional part of brain3.30e-139
collection of basal ganglia3.30e-139
cerebral subcortex3.30e-139
anatomical cluster4.15e-13373
tube6.79e-12192
embryonic structure2.29e-11564
embryo2.42e-11592
germ layer3.55e-11560
germ layer / neural crest3.55e-11560
embryonic tissue3.55e-11560
presumptive structure3.55e-11560
germ layer / neural crest derived structure3.55e-11560
epiblast (generic)3.55e-11560
developing anatomical structure4.22e-11581
posterior neural tube6.16e-1115
chordal neural plate6.16e-1115
anatomical conduit6.92e-11240
organ part9.03e-11218
telencephalic nucleus1.19e-107
multi-tissue structure1.27e-10342
multi-cellular organism1.54e-10656
anatomical system4.07e-10624
anatomical group4.78e-10625
brainstem1.00e-096
limbic system1.38e-085
diencephalon1.73e-087
future diencephalon1.73e-087
temporal lobe7.18e-086
regional part of diencephalon2.77e-074
segmental subdivision of hindbrain3.77e-0712
hindbrain3.77e-0712
presumptive hindbrain3.77e-0712


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.