Coexpression cluster:C4709

Full id: C4709_Osteoblast_anaplastic_neuroblastoma_gastric_osteosarcoma_small_temporal

Phase1 CAGE Peaks

Hg19::chr7:96635329..96635357,+	p9@DLX6
Hg19::chr7:96651945..96651968,-	p@chr7:96651945..96651968 -
Hg19::chr7:96654015..96654018,-	p3@DLX5

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

---

GO ID	GO name	FDR corrected p-value
GO:0030326	embryonic limb morphogenesis	1.67356575388897e-05
GO:0035113	embryonic appendage morphogenesis	1.67356575388897e-05
GO:0048736	appendage development	1.67356575388897e-05
GO:0060173	limb development	1.67356575388897e-05
GO:0035107	appendage morphogenesis	1.67356575388897e-05
GO:0035108	limb morphogenesis	1.67356575388897e-05
GO:0048598	embryonic morphogenesis	9.21430411214545e-05
GO:0001501	skeletal development	0.000409646680478949
GO:0009790	embryonic development	0.000460607511543315
GO:0045669	positive regulation of osteoblast differentiation	0.00256078176098444
GO:0007399	nervous system development	0.00350845721558526
GO:0045667	regulation of osteoblast differentiation	0.00426765549395418
GO:0043565	sequence-specific DNA binding	0.00440434259482924
GO:0009653	anatomical structure morphogenesis	0.0058971223235539
GO:0048513	organ development	0.00653715891505568
GO:0001649	osteoblast differentiation	0.0080000871954273
GO:0042472	inner ear morphogenesis	0.00813161387655096
GO:0042471	ear morphogenesis	0.0088170948994528
GO:0003700	transcription factor activity	0.00890942448432714
GO:0048731	system development	0.00926308952311787
GO:0048839	inner ear development	0.00926308952311787
GO:0043583	ear development	0.00977220537817819
GO:0045597	positive regulation of cell differentiation	0.0104593336467374
GO:0048856	anatomical structure development	0.0126209096667435
GO:0051094	positive regulation of developmental process	0.0139177346613956
GO:0007275	multicellular organismal development	0.0153181195105723
GO:0007423	sensory organ development	0.0155223093697608
GO:0031214	biomineral formation	0.0155223093697608
GO:0001503	ossification	0.0155223093697608
GO:0046849	bone remodeling	0.0163670509123034
GO:0048771	tissue remodeling	0.0173216973689242
GO:0007409	axonogenesis	0.0180455087640718
GO:0048667	neuron morphogenesis during differentiation	0.0180455087640718
GO:0048812	neurite morphogenesis	0.0180455087640718
GO:0000904	cellular morphogenesis during differentiation	0.0184047906051062
GO:0031175	neurite development	0.019169112608058
GO:0045595	regulation of cell differentiation	0.0198917898403947
GO:0048666	neuron development	0.0207102889155031
GO:0032502	developmental process	0.0212452500808942
GO:0006355	regulation of transcription, DNA-dependent	0.0212452500808942
GO:0006351	transcription, DNA-dependent	0.0212833840104711
GO:0032774	RNA biosynthetic process	0.0212833840104711
GO:0003677	DNA binding	0.0212936828766488
GO:0045449	regulation of transcription	0.0212936828766488
GO:0019219	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0212936828766488
GO:0032990	cell part morphogenesis	0.0212936828766488
GO:0030030	cell projection organization and biogenesis	0.0212936828766488
GO:0048858	cell projection morphogenesis	0.0212936828766488
GO:0030182	neuron differentiation	0.0212936828766488
GO:0006350	transcription	0.0212936828766488
GO:0032501	multicellular organismal process	0.0212936828766488
GO:0010468	regulation of gene expression	0.0212936828766488
GO:0031323	regulation of cellular metabolic process	0.0219963890198013
GO:0050793	regulation of developmental process	0.0223070232679849
GO:0048699	generation of neurons	0.0224562671377371
GO:0019222	regulation of metabolic process	0.022827190887131
GO:0016070	RNA metabolic process	0.022827190887131
GO:0022008	neurogenesis	0.0230478209014503
GO:0009888	tissue development	0.0263589672780351
GO:0009887	organ morphogenesis	0.0307377263448293
GO:0010467	gene expression	0.0367545070308573
GO:0000902	cell morphogenesis	0.0383171077563499
GO:0032989	cellular structure morphogenesis	0.0383171077563499
GO:0050794	regulation of cellular process	0.0383171077563499
GO:0006139	nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0396567305998326
GO:0005634	nucleus	0.0419114525788757
GO:0050789	regulation of biological process	0.0424112436476964
GO:0003676	nucleic acid binding	0.0450760257742571
GO:0065007	biological regulation	0.049492041671133

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 term	p-value	n
osteoblast	1.11e-13	11
osteoprogenitor cell	1.11e-13	11
mesenchyme condensation cell	1.11e-13	11
single fate stem cell	7.03e-09	20

Uber Anatomy

Ontology term	p-value	n
cerebral hemisphere	3.35e-17	32
telencephalon	4.17e-17	34
regional part of telencephalon	4.13e-16	33
regional part of forebrain	7.42e-16	41
forebrain	7.42e-16	41
future forebrain	7.42e-16	41
anterior neural tube	2.71e-15	42
gray matter	3.42e-14	34
brain grey matter	3.42e-14	34
regional part of nervous system	1.06e-13	94
nervous system	1.06e-13	94
central nervous system	1.11e-12	82
regional part of cerebral cortex	9.98e-12	22
pre-chordal neural plate	7.81e-11	61
ectoderm	1.65e-10	173
presumptive ectoderm	1.65e-10	173
ectoderm-derived structure	1.89e-10	169
anterior region of body	1.93e-10	129
craniocervical region	1.93e-10	129
neocortex	6.49e-10	20
cerebral cortex	7.72e-10	25
pallium	7.72e-10	25
head	1.29e-09	123
brain	1.96e-09	69
future brain	1.96e-09	69
neural tube	2.62e-09	57
neural rod	2.62e-09	57
future spinal cord	2.62e-09	57
neural keel	2.62e-09	57
regional part of brain	9.35e-09	59
adult organism	2.09e-08	115
telencephalic nucleus	5.14e-08	7
basal ganglion	1.34e-07	9
nuclear complex of neuraxis	1.34e-07	9
aggregate regional part of brain	1.34e-07	9
collection of basal ganglia	1.34e-07	9
cerebral subcortex	1.34e-07	9
parietal lobe	2.63e-07	5
corpus striatum	3.85e-07	4
striatum	3.85e-07	4
ventral part of telencephalon	3.85e-07	4
future corpus striatum	3.85e-07	4

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.