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: KMT2A

Gene summary for KMT2A

Gene summary.

Gene information	Species	Human
	Gene symbol	KMT2A
	Gene ID	4297
	Gene name	lysine methyltransferase 2A
	Gene Alias	ALL-1
	Cytomap	11q23.3
	Gene Type	protein-coding
	GO ID	GO:0002376
	UniProtAcc	Q03164

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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
4297	KMT2A	LZE4T	Human	Esophagus	ESCC	1.04e-13	3.33e-01	0.0811
4297	KMT2A	LZE7T	Human	Esophagus	ESCC	4.17e-02	4.41e-01	0.0667
4297	KMT2A	LZE8T	Human	Esophagus	ESCC	1.40e-03	1.22e-01	0.067
4297	KMT2A	LZE20T	Human	Esophagus	ESCC	1.24e-03	1.94e-01	0.0662
4297	KMT2A	LZE21D1	Human	Esophagus	HGIN	8.48e-03	5.80e-02	0.0632
4297	KMT2A	LZE22D1	Human	Esophagus	HGIN	1.33e-03	3.58e-01	0.0595
4297	KMT2A	LZE22T	Human	Esophagus	ESCC	1.10e-07	9.42e-01	0.068
4297	KMT2A	LZE24T	Human	Esophagus	ESCC	8.22e-17	4.64e-01	0.0596
4297	KMT2A	LZE21T	Human	Esophagus	ESCC	3.47e-09	2.03e-01	0.0655
4297	KMT2A	P1T-E	Human	Esophagus	ESCC	1.06e-06	3.20e-01	0.0875
4297	KMT2A	P2T-E	Human	Esophagus	ESCC	1.01e-19	4.40e-01	0.1177
4297	KMT2A	P4T-E	Human	Esophagus	ESCC	5.35e-24	6.49e-01	0.1323
4297	KMT2A	P5T-E	Human	Esophagus	ESCC	2.98e-06	1.77e-01	0.1327
4297	KMT2A	P8T-E	Human	Esophagus	ESCC	1.56e-11	2.58e-01	0.0889
4297	KMT2A	P9T-E	Human	Esophagus	ESCC	3.18e-10	3.06e-01	0.1131
4297	KMT2A	P10T-E	Human	Esophagus	ESCC	2.66e-24	6.48e-01	0.116
4297	KMT2A	P11T-E	Human	Esophagus	ESCC	3.23e-11	2.85e-01	0.1426
4297	KMT2A	P12T-E	Human	Esophagus	ESCC	5.03e-16	4.89e-01	0.1122
4297	KMT2A	P15T-E	Human	Esophagus	ESCC	4.73e-10	2.10e-01	0.1149
4297	KMT2A	P16T-E	Human	Esophagus	ESCC	1.43e-20	4.64e-01	0.1153

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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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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.

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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:00182057	Esophagus	HGIN	peptidyl-lysine modification	88/2587	376/18723	2.99e-07	1.39e-05	88
GO:005105214	Esophagus	HGIN	regulation of DNA metabolic process	79/2587	359/18723	1.38e-05	3.85e-04	79
GO:00165708	Esophagus	HGIN	histone modification	92/2587	463/18723	1.70e-04	3.30e-03	92
GO:00064735	Esophagus	HGIN	protein acetylation	45/2587	201/18723	6.17e-04	8.58e-03	45
GO:003292210	Esophagus	HGIN	circadian regulation of gene expression	20/2587	68/18723	6.35e-04	8.73e-03	20
GO:00310568	Esophagus	HGIN	regulation of histone modification	36/2587	152/18723	7.06e-04	9.52e-03	36
GO:00439844	Esophagus	HGIN	histone H4-K16 acetylation	9/2587	20/18723	7.18e-04	9.60e-03	9
GO:00183945	Esophagus	HGIN	peptidyl-lysine acetylation	39/2587	169/18723	7.46e-04	9.90e-03	39
GO:00435435	Esophagus	HGIN	protein acylation	51/2587	243/18723	1.33e-03	1.57e-02	51
GO:00439675	Esophagus	HGIN	histone H4 acetylation	19/2587	67/18723	1.39e-03	1.63e-02	19
GO:0018027	Esophagus	HGIN	peptidyl-lysine dimethylation	10/2587	26/18723	1.60e-03	1.79e-02	10
GO:000762318	Esophagus	HGIN	circadian rhythm	45/2587	210/18723	1.60e-03	1.79e-02	45
GO:00064755	Esophagus	HGIN	internal protein amino acid acetylation	36/2587	160/18723	1.87e-03	2.01e-02	36
GO:00310604	Esophagus	HGIN	regulation of histone methylation	19/2587	69/18723	2.03e-03	2.13e-02	19
GO:00515714	Esophagus	HGIN	positive regulation of histone H3-K4 methylation	8/2587	19/18723	2.40e-03	2.41e-02	8
GO:00310624	Esophagus	HGIN	positive regulation of histone methylation	13/2587	41/18723	2.62e-03	2.58e-02	13
GO:00183935	Esophagus	HGIN	internal peptidyl-lysine acetylation	35/2587	158/18723	2.82e-03	2.75e-02	35
GO:00349688	Esophagus	HGIN	histone lysine methylation	27/2587	115/18723	3.51e-03	3.24e-02	27
GO:00064798	Esophagus	HGIN	protein methylation	38/2587	181/18723	5.05e-03	4.22e-02	38
GO:00082138	Esophagus	HGIN	protein alkylation	38/2587	181/18723	5.05e-03	4.22e-02	38

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa052028	Esophagus	ESCC	Transcriptional misregulation in cancer	116/4205	193/8465	2.08e-03	5.95e-03	3.05e-03	116
hsa0031010	Esophagus	ESCC	Lysine degradation	41/4205	63/8465	9.63e-03	2.27e-02	1.16e-02	41
hsa0520213	Esophagus	ESCC	Transcriptional misregulation in cancer	116/4205	193/8465	2.08e-03	5.95e-03	3.05e-03	116
hsa0031013	Esophagus	ESCC	Lysine degradation	41/4205	63/8465	9.63e-03	2.27e-02	1.16e-02	41
hsa003108	Liver	NAFLD	Lysine degradation	21/1043	63/8465	1.09e-05	3.58e-04	2.89e-04	21
hsa0031011	Liver	NAFLD	Lysine degradation	21/1043	63/8465	1.09e-05	3.58e-04	2.89e-04	21
hsa0031021	Liver	Cirrhotic	Lysine degradation	29/2530	63/8465	4.81e-03	1.74e-02	1.07e-02	29
hsa0031031	Liver	Cirrhotic	Lysine degradation	29/2530	63/8465	4.81e-03	1.74e-02	1.07e-02	29
hsa0031041	Liver	HCC	Lysine degradation	47/4020	63/8465	1.02e-05	7.58e-05	4.22e-05	47
hsa0031051	Liver	HCC	Lysine degradation	47/4020	63/8465	1.02e-05	7.58e-05	4.22e-05	47
hsa052026	Lung	IAC	Transcriptional misregulation in cancer	40/1053	193/8465	6.90e-04	5.90e-03	3.92e-03	40
hsa0520211	Lung	IAC	Transcriptional misregulation in cancer	40/1053	193/8465	6.90e-04	5.90e-03	3.92e-03	40
hsa052022	Lung	AIS	Transcriptional misregulation in cancer	39/961	193/8465	2.15e-04	2.41e-03	1.54e-03	39
hsa0031022	Lung	AIS	Lysine degradation	16/961	63/8465	1.41e-03	9.49e-03	6.07e-03	16
hsa052023	Lung	AIS	Transcriptional misregulation in cancer	39/961	193/8465	2.15e-04	2.41e-03	1.54e-03	39
hsa0031032	Lung	AIS	Lysine degradation	16/961	63/8465	1.41e-03	9.49e-03	6.07e-03	16
hsa052027	Prostate	BPH	Transcriptional misregulation in cancer	53/1718	193/8465	9.56e-03	2.92e-02	1.81e-02	53
hsa0520212	Prostate	BPH	Transcriptional misregulation in cancer	53/1718	193/8465	9.56e-03	2.92e-02	1.81e-02	53
hsa0520221	Prostate	Tumor	Transcriptional misregulation in cancer	59/1791	193/8465	1.22e-03	5.26e-03	3.26e-03	59
hsa0520231	Prostate	Tumor	Transcriptional misregulation in cancer	59/1791	193/8465	1.22e-03	5.26e-03	3.26e-03	59

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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

TF	Cell Type	Tissue	Disease Stage	Target Gene	RSS	Regulon Activity
KMT2A	TRANS	Cervix	ADJ	MMP2,ISLR,ASPN, etc.	1.33e-01

∗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

KMT2A

SNV

Missense_Mutation

novel

c.9043N>A

p.Val3015Ile

p.V3015I

Q03164

protein_coding

deleterious_low_confidence(0)

benign(0.012)

TCGA-A1-A0SM-01

Breast

breast invasive carcinoma

Male

>=65

I/II

Unknown

KMT2A

SNV

Missense_Mutation

c.8615N>T

p.Ser2872Leu

p.S2872L

Q03164

protein_coding

deleterious_low_confidence(0.01)

benign(0)

TCGA-A2-A0EY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

KMT2A

SNV

Missense_Mutation

c.9143A>C

p.Lys3048Thr

p.K3048T

Q03164

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.994)

TCGA-A2-A0YJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

KMT2A

SNV

Missense_Mutation

c.10139C>T

p.Ser3380Leu

p.S3380L

Q03164

protein_coding

deleterious_low_confidence(0.01)

possibly_damaging(0.518)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

KMT2A

SNV

Missense_Mutation

novel

c.11231N>A

p.Arg3744Gln

p.R3744Q

Q03164

protein_coding

tolerated(0.22)

possibly_damaging(0.819)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

KMT2A

SNV

Missense_Mutation

novel

c.6203N>A

p.Cys2068Tyr

p.C2068Y

Q03164

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

KMT2A

SNV

Missense_Mutation

rs782339326

c.1838N>A

p.Arg613Gln

p.R613Q

Q03164

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.992)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

KMT2A

SNV

Missense_Mutation

c.6509N>A

p.Ser2170Asn

p.S2170N

Q03164

protein_coding

tolerated(0.11)

benign(0.001)

TCGA-BH-A0HF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

KMT2A

SNV

Missense_Mutation

c.3005N>G

p.Ser1002Cys

p.S1002C

Q03164

protein_coding

deleterious_low_confidence(0)

benign(0.436)

TCGA-C8-A27B-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

KMT2A

SNV

Missense_Mutation

c.5524N>G

p.Thr1842Ala

p.T1842A

Q03164

protein_coding

tolerated(0.5)

benign(0)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

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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
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		DIFLUFENICAN	DIFLUFENICAN
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		GNF-PF-4029	CHEMBL596633
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		CLODRONATE DISODIUM	CLODRONATE DISODIUM
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		METHYLENE BLUE	METHYLENE BLUE
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		TANNIC ACID	TANNIC ACID
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		AMINOQUINURIDE	AMINOQUINURIDE
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		DAUNORUBICIN HYDROCHLORIDE	DAUNORUBICIN HYDROCHLORIDE
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		NSC-95397	CHEMBL429095
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		NSC-69187	CHEMBL19954
4297	KMT2A	METHYL TRANSFERASE, ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME		EMETINE HYDROCHLORIDE	EMETINE HYDROCHLORIDE

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