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

Home

Download

Statistics

Help

Contact

	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: CDK13

Gene summary for CDK13

Gene summary.

Gene information	Species	Human
	Gene symbol	CDK13
	Gene ID	8621
	Gene name	cyclin dependent kinase 13
	Gene Alias	CDC2L
	Cytomap	7p14.1
	Gene Type	protein-coding
	GO ID	GO:0000278
	UniProtAcc	A0A024RA85

Top

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
8621	CDK13	CCI_1	Human	Cervix	CC	1.78e-02	8.73e-01	0.528
8621	CDK13	CCI_2	Human	Cervix	CC	9.89e-12	1.30e+00	0.5249
8621	CDK13	CCI_3	Human	Cervix	CC	9.73e-05	7.08e-01	0.516
8621	CDK13	sample3	Human	Cervix	CC	3.17e-06	2.67e-01	0.1387
8621	CDK13	T3	Human	Cervix	CC	1.27e-04	2.39e-01	0.1389
8621	CDK13	HTA11_3410_2000001011	Human	Colorectum	AD	8.77e-13	-4.72e-01	0.0155
8621	CDK13	HTA11_347_2000001011	Human	Colorectum	AD	4.73e-09	4.95e-01	-0.1954
8621	CDK13	HTA11_2992_2000001011	Human	Colorectum	SER	1.55e-02	-4.86e-01	-0.1706
8621	CDK13	HTA11_5216_2000001011	Human	Colorectum	SER	3.72e-03	-5.75e-01	-0.1462
8621	CDK13	HTA11_7696_3000711011	Human	Colorectum	AD	1.48e-03	-2.78e-01	0.0674
8621	CDK13	HTA11_99999970781_79442	Human	Colorectum	MSS	8.35e-03	-2.76e-01	0.294
8621	CDK13	HTA11_99999965062_69753	Human	Colorectum	MSI-H	5.07e-03	5.19e-01	0.3487
8621	CDK13	HTA11_99999974143_84620	Human	Colorectum	MSS	1.61e-11	-4.52e-01	0.3005
8621	CDK13	A015-C-203	Human	Colorectum	FAP	9.02e-40	-4.78e-01	-0.1294
8621	CDK13	A015-C-204	Human	Colorectum	FAP	1.03e-07	-4.07e-01	-0.0228
8621	CDK13	A014-C-040	Human	Colorectum	FAP	2.08e-08	-6.86e-01	-0.1184
8621	CDK13	A002-C-201	Human	Colorectum	FAP	3.06e-18	-4.38e-01	0.0324
8621	CDK13	A002-C-203	Human	Colorectum	FAP	1.03e-03	-4.38e-04	0.2786
8621	CDK13	A001-C-119	Human	Colorectum	FAP	1.22e-09	-4.29e-01	-0.1557
8621	CDK13	A001-C-108	Human	Colorectum	FAP	1.33e-20	-2.93e-01	-0.0272

Page: 1 2 3 4 5 6 7 8 9 10

Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
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.

Top

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).

Page: 1 2 3 4 5 6 7 8 9

Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:20007375	Esophagus	HGIN	negative regulation of stem cell differentiation	12/2587	23/18723	1.45e-05	4.02e-04	12
GO:20007365	Esophagus	HGIN	regulation of stem cell differentiation	20/2587	58/18723	5.65e-05	1.33e-03	20
GO:00063548	Esophagus	HGIN	DNA-templated transcription, elongation	27/2587	91/18723	6.62e-05	1.52e-03	27
GO:00342435	Esophagus	HGIN	regulation of transcription elongation from RNA polymerase II promoter	13/2587	32/18723	1.72e-04	3.32e-03	13
GO:01400146	Esophagus	HGIN	mitotic nuclear division	61/2587	287/18723	3.38e-04	5.55e-03	61
GO:00327866	Esophagus	HGIN	positive regulation of DNA-templated transcription, elongation	11/2587	27/18723	5.28e-04	7.56e-03	11
GO:00329685	Esophagus	HGIN	positive regulation of transcription elongation from RNA polymerase II promoter	7/2587	13/18723	7.61e-04	1.00e-02	7
GO:00327844	Esophagus	HGIN	regulation of DNA-templated transcription, elongation	16/2587	53/18723	1.58e-03	1.79e-02	16
GO:00708162	Esophagus	HGIN	phosphorylation of RNA polymerase II C-terminal domain	6/2587	12/18723	3.03e-03	2.88e-02	6
GO:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:0000375111	Esophagus	ESCC	RNA splicing, via transesterification reactions	248/8552	324/18723	3.05e-30	1.49e-27	248
GO:0000377111	Esophagus	ESCC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:0000398111	Esophagus	ESCC	mRNA splicing, via spliceosome	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:014001414	Esophagus	ESCC	mitotic nuclear division	218/8552	287/18723	6.17e-26	1.78e-23	218
GO:000734615	Esophagus	ESCC	regulation of mitotic cell cycle	293/8552	457/18723	8.00e-16	5.64e-14	293
GO:000635414	Esophagus	ESCC	DNA-templated transcription, elongation	76/8552	91/18723	8.35e-14	4.11e-12	76
GO:00482853	Esophagus	ESCC	organelle fission	301/8552	488/18723	4.64e-13	2.12e-11	301
GO:00002802	Esophagus	ESCC	nuclear division	270/8552	439/18723	1.17e-11	4.24e-10	270
GO:000636814	Esophagus	ESCC	transcription elongation from RNA polymerase II promoter	56/8552	69/18723	1.40e-09	3.30e-08	56
GO:003278412	Esophagus	ESCC	regulation of DNA-templated transcription, elongation	45/8552	53/18723	3.64e-09	7.61e-08	45

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Enriched KEGG pathways.

Pathway ID

Tissue

Disease Stage

Description

Gene Ratio

Bg Ratio

pvalue

p.adjust

qvalue

Count

Page: 1

Top

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

Page: 1

Top

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.

Page: 1

Top

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

CDK13

SNV

Missense_Mutation

c.1738N>G

p.Leu580Val

p.L580V

Q14004

protein_coding

tolerated(0.95)

benign(0)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CDK13

SNV

Missense_Mutation

c.2522N>T

p.Ser841Phe

p.S841F

Q14004

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CDK13

SNV

Missense_Mutation

c.2045N>A

p.Ile682Lys

p.I682K

Q14004

protein_coding

deleterious(0.01)

probably_damaging(0.96)

TCGA-AN-A0FW-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

CDK13

SNV

Missense_Mutation

c.2866N>C

p.Tyr956His

p.Y956H

Q14004

protein_coding

tolerated(0.1)

possibly_damaging(0.673)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CDK13

SNV

Missense_Mutation

c.1865N>T

p.Ala622Val

p.A622V

Q14004

protein_coding

tolerated(0.42)

benign(0.025)

TCGA-D8-A1XC-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

CDK13

SNV

Missense_Mutation

novel

c.3716N>G

p.Asp1239Gly

p.D1239G

Q14004

protein_coding

deleterious_low_confidence(0.02)

benign(0.154)

TCGA-GM-A3XL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

CDK13

SNV

Missense_Mutation

novel

c.3806C>T

p.Pro1269Leu

p.P1269L

Q14004

protein_coding

deleterious_low_confidence(0.04)

probably_damaging(0.923)

TCGA-LD-A74U-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

taxotere

CDK13

SNV

Missense_Mutation

novel

c.2159N>G

p.Tyr720Cys

p.Y720C

Q14004

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-LL-A73Y-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

taxotere

CDK13

insertion

In_Frame_Ins

novel

c.1809_1810insGTCTGGAAA

p.Val603_Thr604insValTrpLys

p.V603_T604insVWK

Q14004

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CDK13

insertion

Frame_Shift_Ins

novel

c.3817_3818insTAAATGTCTCCAT

p.Glu1273ValfsTer25

p.E1273Vfs*25

Q14004

protein_coding

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14

Top

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
8621	CDK13	ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	375973251
8621	CDK13	ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	CHEMBL3544942	RONICICLIB
8621	CDK13	ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	CHEMBL488436	AZD-5438
8621	CDK13	ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	CHEMBL445813	AT-7519
8621	CDK13	ENZYME, KINASE, DRUGGABLE GENOME, SERINE THREONINE KINASE	inhibitor	CHEMBL1230607	PHA-793887

Page: 1