Coexpression cluster:C4226

Full id: C4226_pineal_Neutrophils_Fibroblast_liposarcoma_parietal_clear_paracentral

Phase1 CAGE Peaks

Hg19::chr2:40679152..40679180,-	p3@SLC8A1
Hg19::chr2:40679186..40679297,-	p1@SLC8A1
Hg19::chr2:40679461..40679475,-	p4@SLC8A1

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

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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

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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>

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Cell Type

Ontology term	p-value	n
macrophage dendritic cell progenitor	3.10e-19	61
myeloid leukocyte	3.35e-18	72
monopoietic cell	3.63e-18	59
monocyte	3.63e-18	59
monoblast	3.63e-18	59
promonocyte	3.63e-18	59
classical monocyte	4.29e-18	42
CD14-positive, CD16-negative classical monocyte	4.29e-18	42
defensive cell	8.88e-18	48
phagocyte	8.88e-18	48
granulocyte monocyte progenitor cell	1.63e-16	67
myeloid lineage restricted progenitor cell	7.26e-14	66
stuff accumulating cell	5.01e-09	87
skin fibroblast	3.01e-07	23
myeloid cell	3.13e-07	108
common myeloid progenitor	3.13e-07	108

Uber Anatomy

Ontology term	p-value	n
neural tube	6.75e-28	56
neural rod	6.75e-28	56
future spinal cord	6.75e-28	56
neural keel	6.75e-28	56
central nervous system	5.72e-27	81
regional part of nervous system	9.39e-27	53
regional part of brain	9.39e-27	53
brain	6.11e-26	68
future brain	6.11e-26	68
adult organism	1.78e-25	114
regional part of forebrain	1.87e-25	41
forebrain	1.87e-25	41
anterior neural tube	1.87e-25	41
future forebrain	1.87e-25	41
nervous system	1.70e-24	89
cerebral hemisphere	6.44e-23	32
telencephalon	4.48e-22	34
brain grey matter	6.10e-22	34
gray matter	6.10e-22	34
neural plate	6.52e-21	82
presumptive neural plate	6.52e-21	82
regional part of telencephalon	7.12e-21	32
cerebral cortex	1.49e-18	25
pallium	1.49e-18	25
neurectoderm	1.49e-18	86
pre-chordal neural plate	2.68e-18	61
regional part of cerebral cortex	5.11e-18	22
neocortex	1.19e-16	20
multi-cellular organism	1.30e-16	656
anatomical system	3.52e-16	624
hematopoietic system	3.73e-16	98
blood island	3.73e-16	98
anatomical group	5.59e-16	625
skeletal system	1.20e-15	100
bone element	1.30e-15	82
bone marrow	1.93e-15	76
organ	4.48e-14	503
ecto-epithelium	9.36e-14	104
skeletal element	1.24e-13	90
structure with developmental contribution from neural crest	1.93e-13	132
tissue	1.12e-12	773
hemolymphoid system	1.50e-12	108
germ layer	8.25e-12	560
germ layer / neural crest	8.25e-12	560
embryonic tissue	8.25e-12	560
presumptive structure	8.25e-12	560
germ layer / neural crest derived structure	8.25e-12	560
epiblast (generic)	8.25e-12	560
embryonic structure	1.33e-11	564
ectoderm-derived structure	4.34e-11	171
ectoderm	4.34e-11	171
presumptive ectoderm	4.34e-11	171
musculoskeletal system	5.67e-11	167
immune system	7.53e-11	93
developing anatomical structure	2.51e-10	581
embryo	5.75e-10	592
organ system subdivision	3.94e-07	223

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

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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

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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

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This analysis result is provided for C0 - C305 clusters.