Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: NOP14

Gene summary for NOP14

Gene summary.

Gene information	Species	Human
	Gene symbol	NOP14
	Gene ID	8602
	Gene name	NOP14 nucleolar protein
	Gene Alias	C4orf9
	Cytomap	4p16.3
	Gene Type	protein-coding
	GO ID	GO:0000447
	UniProtAcc	A8KA74

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
8602	NOP14	P62T-E	Human	Esophagus	ESCC	5.28e-31	7.39e-01	0.1302
8602	NOP14	P65T-E	Human	Esophagus	ESCC	1.77e-14	2.02e-01	0.0978
8602	NOP14	P74T-E	Human	Esophagus	ESCC	4.08e-05	1.87e-01	0.1479
8602	NOP14	P75T-E	Human	Esophagus	ESCC	1.15e-17	5.00e-01	0.1125
8602	NOP14	P76T-E	Human	Esophagus	ESCC	7.58e-14	4.17e-01	0.1207
8602	NOP14	P79T-E	Human	Esophagus	ESCC	4.00e-15	3.10e-01	0.1154
8602	NOP14	P80T-E	Human	Esophagus	ESCC	6.76e-24	1.09e+00	0.155
8602	NOP14	P82T-E	Human	Esophagus	ESCC	2.49e-02	4.34e-01	0.1072
8602	NOP14	P83T-E	Human	Esophagus	ESCC	7.29e-20	7.57e-01	0.1738
8602	NOP14	P89T-E	Human	Esophagus	ESCC	4.19e-06	4.67e-01	0.1752
8602	NOP14	P107T-E	Human	Esophagus	ESCC	1.70e-47	1.29e+00	0.171
8602	NOP14	P126T-E	Human	Esophagus	ESCC	6.33e-04	5.12e-01	0.1125
8602	NOP14	P127T-E	Human	Esophagus	ESCC	1.94e-08	7.52e-02	0.0826
8602	NOP14	P128T-E	Human	Esophagus	ESCC	3.65e-28	1.06e+00	0.1241
8602	NOP14	P130T-E	Human	Esophagus	ESCC	4.66e-29	6.94e-01	0.1676
8602	NOP14	HCC1_Meng	Human	Liver	HCC	1.53e-45	1.19e-01	0.0246
8602	NOP14	HCC2_Meng	Human	Liver	HCC	9.15e-11	9.52e-02	0.0107
8602	NOP14	HCC1	Human	Liver	HCC	1.11e-04	2.98e+00	0.5336
8602	NOP14	HCC2	Human	Liver	HCC	4.60e-18	4.10e+00	0.5341
8602	NOP14	HCC5	Human	Liver	HCC	1.53e-06	2.44e+00	0.4932

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0022613111	Esophagus	ESCC	ribonucleoprotein complex biogenesis	365/8552	463/18723	1.74e-49	1.11e-45	365
GO:0042254111	Esophagus	ESCC	ribosome biogenesis	252/8552	299/18723	3.27e-44	1.04e-40	252
GO:003447015	Esophagus	ESCC	ncRNA processing	300/8552	395/18723	3.09e-35	3.26e-32	300
GO:0016072110	Esophagus	ESCC	rRNA metabolic process	197/8552	236/18723	1.31e-33	1.18e-30	197
GO:0006364110	Esophagus	ESCC	rRNA processing	189/8552	225/18723	4.88e-33	3.87e-30	189
GO:003466012	Esophagus	ESCC	ncRNA metabolic process	346/8552	485/18723	4.35e-31	2.51e-28	346
GO:0042274111	Esophagus	ESCC	ribosomal small subunit biogenesis	67/8552	73/18723	6.62e-17	5.38e-15	67
GO:00905013	Esophagus	ESCC	RNA phosphodiester bond hydrolysis	110/8552	152/18723	1.95e-11	6.81e-10	110
GO:00304904	Esophagus	ESCC	maturation of SSU-rRNA	45/8552	50/18723	5.07e-11	1.63e-09	45
GO:00903053	Esophagus	ESCC	nucleic acid phosphodiester bond hydrolysis	163/8552	261/18723	3.07e-08	5.73e-07	163
GO:00004623	Esophagus	ESCC	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	32/8552	37/18723	2.96e-07	4.23e-06	32
GO:00004603	Esophagus	ESCC	maturation of 5.8S rRNA	30/8552	35/18723	1.07e-06	1.34e-05	30
GO:00004693	Esophagus	ESCC	cleavage involved in rRNA processing	24/8552	27/18723	3.48e-06	3.84e-05	24
GO:00004663	Esophagus	ESCC	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	21/8552	24/18723	2.57e-05	2.17e-04	21
GO:00905023	Esophagus	ESCC	RNA phosphodiester bond hydrolysis, endonucleolytic	55/8552	82/18723	7.34e-05	5.51e-04	55
GO:00004783	Esophagus	ESCC	endonucleolytic cleavage involved in rRNA processing	14/8552	15/18723	1.47e-04	9.85e-04	14
GO:00004793	Esophagus	ESCC	endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	14/8552	15/18723	1.47e-04	9.85e-04	14
GO:00344713	Esophagus	ESCC	ncRNA 5'-end processing	18/8552	21/18723	1.81e-04	1.16e-03	18
GO:00009663	Esophagus	ESCC	RNA 5'-end processing	19/8552	23/18723	3.12e-04	1.85e-03	19
GO:002261322	Liver	HCC	ribonucleoprotein complex biogenesis	355/7958	463/18723	7.76e-52	4.92e-48	355

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Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

NOP14

SNV

Missense_Mutation

novel

c.418C>A

p.His140Asn

p.H140N

P78316

protein_coding

deleterious(0.01)

benign(0.359)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

NOP14

SNV

Missense_Mutation

c.718G>C

p.Glu240Gln

p.E240Q

P78316

protein_coding

tolerated(0.15)

benign(0.027)

TCGA-C8-A1HG-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NOP14

SNV

Missense_Mutation

c.727G>C

p.Asp243His

p.D243H

P78316

protein_coding

deleterious(0.01)

benign(0.015)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

NOP14

SNV

Missense_Mutation

c.1066N>A

p.Glu356Lys

p.E356K

P78316

protein_coding

tolerated(0.17)

benign(0.012)

TCGA-E2-A10C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

NOP14

SNV

Missense_Mutation

c.2571A>T

p.Lys857Asn

p.K857N

P78316

protein_coding

deleterious_low_confidence(0.03)

benign(0.006)

TCGA-E2-A1IH-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

aromasin

NOP14

insertion

Frame_Shift_Ins

novel

c.840_841insTTCAGGCGGGGAGGACACAGAGGAGAGCGACAGCC

p.Glu281PhefsTer49

p.E281Ffs*49

P78316

protein_coding

TCGA-BH-A0HK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

NOP14

SNV

Missense_Mutation

rs770027682

c.2238N>C

p.Gln746His

p.Q746H

P78316

protein_coding

tolerated(0.16)

possibly_damaging(0.69)

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

NOP14

SNV

Missense_Mutation

novel

c.1240N>C

p.Ala414Pro

p.A414P

P78316

protein_coding

tolerated(0.14)

possibly_damaging(0.602)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NOP14

SNV

Missense_Mutation

c.1483N>T

p.Ile495Phe

p.I495F

P78316

protein_coding

tolerated(0.14)

possibly_damaging(0.899)

TCGA-JX-A3Q8-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NOP14

SNV

Missense_Mutation

novel

c.2363N>G

p.Glu788Gly

p.E788G

P78316

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-VS-A954-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID

Symbol

Category

Interaction Types

Drug Claim Name

Drug Name

PMIDs

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