Coexpression cluster:C2548

Full id: C2548_salivary_immature_tongue_esophagus_amniotic_cervical_Corneal

Phase1 CAGE Peaks

Hg19::chr1:201252522..201252533,+	p2@PKP1
Hg19::chr1:201252623..201252640,+	p1@PKP1
Hg19::chr2:64681348..64681364,+	p1@LGALSL
Hg19::chr6:7541895..7541916,+	p1@DSP

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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p.value	FDR	nGenes	nPathway	Name
2.63387331172458e-05	0.0166724180632166	2	147	Apoptosis (Reactome):REACT_578

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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GO ID	GO name	FDR corrected p-value
GO:0005911	intercellular junction	0.00104122004525117
GO:0005882	intermediate filament	0.00104122004525117
GO:0045111	intermediate filament cytoskeleton	0.00104122004525117
GO:0019215	intermediate filament binding	0.00191331223659601
GO:0030054	cell junction	0.00206830683319861
GO:0030280	structural constituent of epidermis	0.00546596270161619
GO:0030057	desmosome	0.00546596270161619
GO:0044430	cytoskeletal part	0.00552645155524017
GO:0005913	cell-cell adherens junction	0.00552645155524017
GO:0001533	cornified envelope	0.00841609563968864
GO:0018149	peptide cross-linking	0.00882703254456832
GO:0005856	cytoskeleton	0.00882703254456832
GO:0030216	keratinocyte differentiation	0.00882703254456832
GO:0014704	intercalated disc	0.012838016257695
GO:0005912	adherens junction	0.0137653044832711
GO:0044459	plasma membrane part	0.0175034631324322
GO:0007275	multicellular organismal development	0.0175034631324322
GO:0005200	structural constituent of cytoskeleton	0.0180480957314749
GO:0030674	protein binding, bridging	0.0182357472300847
GO:0032403	protein complex binding	0.0182357472300847
GO:0043296	apical junction complex	0.0182357472300847
GO:0016327	apicolateral plasma membrane	0.0182357472300847
GO:0043232	intracellular non-membrane-bound organelle	0.0200027457430974
GO:0043228	non-membrane-bound organelle	0.0200027457430974
GO:0008544	epidermis development	0.0206233211507383
GO:0007398	ectoderm development	0.0214424247473283
GO:0032502	developmental process	0.0233615575638312
GO:0005886	plasma membrane	0.0283630958363565
GO:0032501	multicellular organismal process	0.0283630958363565
GO:0044446	intracellular organelle part	0.0309825493835566
GO:0044422	organelle part	0.0309825493835566
GO:0009888	tissue development	0.0363098561462876

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>

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Cell Type

Ontology term	p-value	n
epithelial cell	2.02e-23	253
endodermal cell	3.22e-15	58
endo-epithelial cell	1.11e-14	42
epithelial cell of alimentary canal	4.39e-08	20
respiratory epithelial cell	5.98e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	8.29e-19	160
endoderm	8.29e-19	160
presumptive endoderm	8.29e-19	160
digestive system	4.73e-15	145
digestive tract	4.73e-15	145
primitive gut	4.73e-15	145
multi-cellular organism	4.60e-14	656
subdivision of digestive tract	1.98e-13	118
organ	1.24e-11	503
multi-tissue structure	2.33e-11	342
adult organism	4.09e-11	114
organism subdivision	6.56e-11	264
respiratory system	1.48e-10	74
foregut	1.68e-10	87
organ part	9.31e-10	218
embryo	1.36e-09	592
anatomical system	1.94e-09	624
anatomical group	2.07e-09	625
renal system	8.00e-09	48
developing anatomical structure	9.85e-09	581
subdivision of trunk	1.03e-08	112
immaterial anatomical entity	1.48e-08	117
trunk region element	1.66e-08	101
urinary system structure	1.79e-08	47
endo-epithelium	3.50e-08	82
organ system subdivision	7.29e-08	223
anatomical cluster	9.35e-08	373
anterior region of body	1.95e-07	62
craniocervical region	1.95e-07	62
gland	4.01e-07	59
primordium	4.48e-07	160
head	6.22e-07	56
anatomical space	6.96e-07	95
respiratory tract	8.23e-07	54
exocrine gland	8.57e-07	31
exocrine system	8.57e-07	31
orifice	9.23e-07	36

Disease

Ontology term	p-value	n
carcinoma	2.45e-12	106
cell type cancer	8.39e-07	143

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)
MA0003.1	1.45381
MA0004.1	0.71247
MA0006.1	0.532262
MA0007.1	0.6918
MA0009.1	1.20602
MA0014.1	0.896009
MA0017.1	0.577281
MA0019.1	0.873355
MA0024.1	1.09684
MA0025.1	1.34373
MA0027.1	2.83281
MA0028.1	0.550763
MA0029.1	1.11704
MA0030.1	1.10506
MA0031.1	1.03735
MA0038.1	0.824639
MA0040.1	1.12314
MA0041.1	0.732902
MA0042.1	0.697662
MA0043.1	1.20635
MA0046.1	1.19471
MA0048.1	2.02223
MA0050.1	0.69864
MA0051.1	0.820063
MA0052.1	1.12718
MA0055.1	4.83833
MA0056.1	0
MA0057.1	0.248209
MA0058.1	0.605914
MA0059.1	0.604454
MA0060.1	0.393285
MA0061.1	0.360128
MA0063.1	0
MA0066.1	0.825101
MA0067.1	1.53181
MA0068.1	0.313194
MA0069.1	1.19071
MA0070.1	1.17908
MA0071.1	0.782546
MA0072.1	1.1744
MA0073.1	0.866596
MA0074.1	0.819248
MA0076.1	0.623864
MA0077.1	1.16637
MA0078.1	0.926725
MA0081.1	0.604638
MA0083.1	1.21381
MA0084.1	1.72172
MA0087.1	1.17185
MA0088.1	0.182167
MA0089.1	0
MA0090.1	0.640115
MA0091.1	0.715356
MA0092.1	0.673508
MA0093.1	0.535768
MA0095.1	0
MA0098.1	0
MA0100.1	0.83965
MA0101.1	0.539569
MA0103.1	1.29536
MA0105.1	1.22348
MA0106.1	0.869173
MA0107.1	0.453492
MA0108.2	1.03412
MA0109.1	0
MA0111.1	0.655276
MA0113.1	0.886811
MA0114.1	0.447443
MA0115.1	1.45393
MA0116.1	0.457606
MA0117.1	1.24497
MA0119.1	0.586221
MA0122.1	1.27173
MA0124.1	1.41151
MA0125.1	1.32534
MA0130.1	0
MA0131.1	0.94608
MA0132.1	0
MA0133.1	0
MA0135.1	1.23748
MA0136.1	0.832277
MA0139.1	0.344952
MA0140.1	0.779643
MA0141.1	0.602484
MA0142.1	1.00381
MA0143.1	0.887001
MA0144.1	0.430413
MA0145.1	0.195821
MA0146.1	1.75643
MA0147.1	0.46175
MA0148.1	0.739888
MA0149.1	0.769072
MA0062.2	0.353589
MA0035.2	0.778873
MA0039.2	3.66694
MA0138.2	0.928035
MA0002.2	0.379056
MA0137.2	0.558189
MA0104.2	0.392359
MA0047.2	0.856092
MA0112.2	1.65877
MA0065.2	1.09513
MA0150.1	0.633493
MA0151.1	0
MA0152.1	0.78681
MA0153.1	1.30799
MA0154.1	1.21162
MA0155.1	0.180766
MA0156.1	0.560797
MA0157.1	0.97481
MA0158.1	0
MA0159.1	0.462502
MA0160.1	0.756582
MA0161.1	0
MA0162.1	0.640035
MA0163.1	0.539587
MA0164.1	0.90014
MA0080.2	0.535868
MA0018.2	0.870662
MA0099.2	0.7872
MA0079.2	3.5408
MA0102.2	1.75932
MA0258.1	0.418966
MA0259.1	0.471671
MA0442.1	0

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
BHLHE40#8553	2	22.4359067734887	0.00289146449685312	0.0156402351660888

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.