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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1757_caudate_neuroectodermal_middle_hippocampus_occipital_medial_parietal
|full_id=C1757_caudate_neuroectodermal_middle_hippocampus_occipital_medial_parietal
|id=C1757
|id=C1757

Revision as of 14:21, 12 September 2012


Full id: C1757_caudate_neuroectodermal_middle_hippocampus_occipital_medial_parietal



Phase1 CAGE Peaks

Hg19::chr16:24228211..24228225,+p9@PRKCB
Hg19::chr16:24228276..24228319,+p6@PRKCB
Hg19::chr16:24228354..24228378,+p8@PRKCB
Hg19::chr16:24230796..24230825,+p@chr16:24230796..24230825
+
Hg19::chr16:24230834..24230957,+p@chr16:24230834..24230957
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
hematopoietic stem cell5.53e-54172
angioblastic mesenchymal cell5.53e-54172
hematopoietic oligopotent progenitor cell6.76e-53165
hematopoietic multipotent progenitor cell6.76e-53165
hematopoietic cell6.81e-50182
leukocyte2.82e-43140
hematopoietic lineage restricted progenitor cell1.32e-37124
nongranular leukocyte1.19e-36119
myeloid cell8.86e-32112
common myeloid progenitor8.86e-32112
myeloid leukocyte1.45e-2076
lymphocyte1.67e-1853
common lymphoid progenitor1.67e-1853
granulocyte monocyte progenitor cell1.90e-1871
myeloid lineage restricted progenitor cell4.42e-1870
lymphoid lineage restricted progenitor cell6.51e-1852
macrophage dendritic cell progenitor2.81e-1765
monopoietic cell2.95e-1663
monocyte2.95e-1663
monoblast2.95e-1663
promonocyte2.95e-1663
CD14-positive, CD16-negative classical monocyte4.32e-1442
classical monocyte5.84e-1445
lymphocyte of B lineage2.18e-1124
pro-B cell2.18e-1124
mature alpha-beta T cell5.46e-0818
alpha-beta T cell5.46e-0818
immature T cell5.46e-0818
mature T cell5.46e-0818
immature alpha-beta T cell5.46e-0818
B cell6.62e-0714
Uber Anatomy
Ontology termp-valuen
adult organism2.53e-32115
neural tube1.47e-2457
neural rod1.47e-2457
future spinal cord1.47e-2457
neural keel1.47e-2457
hematopoietic system8.17e-24102
blood island8.17e-24102
regional part of forebrain5.38e-2341
forebrain5.38e-2341
future forebrain5.38e-2341
anterior neural tube6.63e-2342
telencephalon2.98e-2134
gray matter4.22e-2134
brain grey matter4.22e-2134
hemolymphoid system6.06e-21112
cerebral hemisphere1.02e-2032
regional part of telencephalon1.52e-2033
regional part of brain2.04e-1959
central nervous system2.95e-1882
regional part of cerebral cortex3.78e-1822
brain8.80e-1769
future brain8.80e-1769
neocortex1.71e-1620
neurectoderm1.34e-1590
regional part of nervous system1.82e-1594
nervous system1.82e-1594
cerebral cortex2.17e-1525
pallium2.17e-1525
bone marrow4.52e-1580
neural plate1.92e-1386
presumptive neural plate1.92e-1386
bone element6.87e-1386
pre-chordal neural plate1.16e-1161
immune system9.06e-10115
skeletal element5.22e-09101
skeletal system5.22e-09101
basal ganglion4.40e-089
nuclear complex of neuraxis4.40e-089
aggregate regional part of brain4.40e-089
collection of basal ganglia4.40e-089
cerebral subcortex4.40e-089
blood1.43e-0715
haemolymphatic fluid1.43e-0715
organism substance1.43e-0715
nucleus of brain3.39e-079
neural nucleus3.39e-079
temporal lobe6.07e-077
Disease
Ontology termp-valuen
hematologic cancer1.76e-1151
immune system cancer1.76e-1151
myeloid leukemia2.06e-1131
leukemia7.73e-1139


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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