Coexpression cluster:C221

Full id: C221_alveolar_Osteoblast_Myoblast_mesenchymal_liposarcoma_Smooth_hepatocellular

Phase1 CAGE Peaks

Hg19::chr10:101690855..101690861,-	p14@DNMBP
Hg19::chr10:101691056..101691064,-	p13@DNMBP
Hg19::chr10:101691084..101691100,-	p8@DNMBP
Hg19::chr10:101691101..101691115,-	p7@DNMBP
Hg19::chr10:101691118..101691135,-	p6@DNMBP
Hg19::chr10:101691199..101691208,-	p11@DNMBP
Hg19::chr11:104005546..104005596,-	p@chr11:104005546..104005596 -
Hg19::chr11:47256459..47256470,+	p@chr11:47256459..47256470 +
Hg19::chr12:20910262..20910266,-	p@chr12:20910262..20910266 -
Hg19::chr12:92081022..92081033,-	p@chr12:92081022..92081033 -
Hg19::chr13:24144882..24144893,+	p8@TNFRSF19
Hg19::chr13:24144896..24144956,+	p3@TNFRSF19
Hg19::chr13:24144958..24144969,+	p10@TNFRSF19
Hg19::chr14:29047309..29047323,+	p@chr14:29047309..29047323 +
Hg19::chr15:79290919..79290969,+	p@chr15:79290919..79290969 +
Hg19::chr16:11118533..11118538,+	p12@CLEC16A
Hg19::chr16:15991751..15991767,-	p@chr16:15991751..15991767 -
Hg19::chr17:13574618..13574636,-	p@chr17:13574618..13574636 -
Hg19::chr17:40481474..40481498,-	p@chr17:40481474..40481498 -
Hg19::chr17:63511856..63511858,-	p@chr17:63511856..63511858 -
Hg19::chr18:20715474..20715486,+	p4@CABLES1
Hg19::chr18:56199164..56199168,-	p@chr18:56199164..56199168 -
Hg19::chr1:114430113..114430124,-	p4@BCL2L15
Hg19::chr1:145683530..145683562,+	p@chr1:145683530..145683562 +
Hg19::chr1:219980111..219980117,-	p@chr1:219980111..219980117 -
Hg19::chr1:246033769..246033788,-	p@chr1:246033769..246033788 -
Hg19::chr20:2779140..2779150,-	p9@CPXM1
Hg19::chr20:2779199..2779205,-	p13@CPXM1
Hg19::chr20:2779236..2779242,-	p12@CPXM1
Hg19::chr20:2779313..2779314,-	p16@CPXM1
Hg19::chr2:75751179..75751194,+	p1@BC018659
Hg19::chr3:165178296..165178305,+	p@chr3:165178296..165178305 +
Hg19::chr3:165178316..165178330,+	p@chr3:165178316..165178330 +
Hg19::chr3:165178334..165178342,+	p@chr3:165178334..165178342 +
Hg19::chr3:55001120..55001131,-	p6@LRTM1
Hg19::chr3:55002066..55002104,+	p@chr3:55002066..55002104 +
Hg19::chr3:55002159..55002164,+	p@chr3:55002159..55002164 +
Hg19::chr3:55002193..55002225,+	p@chr3:55002193..55002225 +
Hg19::chr3:55002230..55002244,+	p@chr3:55002230..55002244 +
Hg19::chr5:179720177..179720223,+	p1@ENST00000504573
Hg19::chr5:179757790..179757847,-	p2@GFPT2
Hg19::chr5:179757851..179757870,-	p4@GFPT2
Hg19::chr5:179757923..179757948,-	p3@GFPT2
Hg19::chr5:81683619..81683623,+	p@chr5:81683619..81683623 +
Hg19::chr6:137314390..137314394,-	p1@ENST00000418699 p1@ENST00000432330
Hg19::chr6:139013065..139013100,+	p6@FLJ46906
Hg19::chr6:73785930..73785949,-	p@chr6:73785930..73785949 -
Hg19::chr6:73786593..73786601,+	p@chr6:73786593..73786601 +
Hg19::chr6:73786620..73786627,+	p@chr6:73786620..73786627 +
Hg19::chr7:40832998..40833012,+	p3@C7orf10
Hg19::chr7:40833016..40833066,+	p2@C7orf10
Hg19::chr7:43733671..43733688,-	p@chr7:43733671..43733688 -
Hg19::chr7:63539651..63539654,+	p1@ENST00000430271
Hg19::chr8:123580859..123580902,-	p@chr8:123580859..123580902 -
Hg19::chr8:123580905..123580931,-	p@chr8:123580905..123580931 -
Hg19::chr8:123580943..123580958,-	p@chr8:123580943..123580958 -
Hg19::chr8:123580969..123580991,-	p@chr8:123580969..123580991 -
Hg19::chr8:123580995..123581003,-	p@chr8:123580995..123581003 -
Hg19::chr8:123581008..123581037,-	p@chr8:123581008..123581037 -
Hg19::chr8:32579421..32579432,+	p26@NRG1
Hg19::chr8:94870047..94870056,+	p30@PDP1
Hg19::chr9:119051028..119051054,-	p1@ENST00000438048
Hg19::chr9:140350189..140350212,-	p30@NELF
Hg19::chr9:140351903..140351920,-	p6@NELF
Hg19::chrX:29686367..29686386,+	p@chrX:29686367..29686386 +

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:0019887	protein kinase regulator activity	0.0272063216252323
GO:0051302	regulation of cell division	0.0272063216252323
GO:0004360	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	0.0272063216252323
GO:0019207	kinase regulator activity	0.0272063216252323
GO:0030297	transmembrane receptor protein tyrosine kinase activator activity	0.0292212530700774
GO:0030971	receptor tyrosine kinase binding	0.0292212530700774
GO:0006002	fructose 6-phosphate metabolic process	0.0292212530700774
GO:0030296	protein tyrosine kinase activator activity	0.0383416067561451
GO:0005031	tumor necrosis factor receptor activity	0.0454285307791918
GO:0043120	tumor necrosis factor binding	0.0459896188608919
GO:0005035	death receptor activity	0.0464473247508643
GO:0016538	cyclin-dependent protein kinase regulator activity	0.0468274943289149
GO:0030295	protein kinase activator activity	0.0471480208963674

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 term	p-value	n
pneumocyte	2.39e-66	3
epithelial cell of tracheobronchial tree	2.62e-23	9
epithelial cell of lower respiratory tract	2.62e-23	9
respiratory epithelial cell	1.21e-16	13
epithelial cell of lung	6.95e-12	19

Uber Anatomy

Ontology term	p-value	n
bronchoalveolar duct junction	1.55e-98	2
alveolar duct	1.55e-98	2
bronchiole	1.55e-98	2
pulmonary alveolus epithelium	2.39e-66	3
alveolus	2.39e-66	3
pulmonary lobule	2.39e-66	3
lobule	2.39e-66	3
alveolus of lung	2.39e-66	3
alveolar system	2.39e-66	3
pulmonary acinus	2.39e-66	3
alveolar sac	2.39e-66	3
alveolar wall	2.39e-66	3
anatomical wall	6.76e-18	12
tracheobronchial tree	1.22e-14	15
lower respiratory tract	1.22e-14	15
duct	6.95e-12	19
respiratory tract epithelium	6.95e-12	19
lung epithelium	6.95e-12	19
lung	1.80e-10	22
simple squamous epithelium	1.80e-10	22
respiratory tube	1.80e-10	22
respiration organ	1.80e-10	22
pair of lungs	1.80e-10	22
lung primordium	1.80e-10	22
lung bud	1.80e-10	22
epithelial sac	2.15e-09	25
squamous epithelium	2.15e-09	25
sac	4.34e-09	26
respiratory system epithelium	1.52e-08	28
thoracic cavity element	2.74e-07	34
thoracic cavity	2.74e-07	34
thoracic segment organ	4.03e-07	35
epithelial bud	8.21e-07	37

Disease

Ontology term	p-value	n
lung adenocarcinoma	1.55e-98	2
non-small cell lung carcinoma	1.48e-40	5
bronchus cancer	1.78e-29	7
bronchogenic carcinoma	1.78e-29	7
lung carcinoma	2.62e-23	9
lung cancer	1.22e-14	15
respiratory system cancer	8.02e-14	16

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	#promoters	Enrichment	p-value	q-value
JUN#3725	16	3.08008103195971	3.99486758543661e-05	0.000741988219376515
STAT3#6774	19	3.0749205376297	6.20075441492697e-06	0.000183196772373567
TCF7L2#6934	19	3.14820545691707	4.39975432367538e-06	0.000137782891097551

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

---