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: MLPH

Gene summary for MLPH

Gene summary.

Gene information	Species	Human
	Gene symbol	MLPH
	Gene ID	79083
	Gene name	melanophilin
	Gene Alias	SLAC2-A
	Cytomap	2q37.3
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	A0A024R4D3

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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
79083	MLPH	GSM4909281	Human	Breast	IDC	8.25e-07	-2.21e-01	0.21
79083	MLPH	GSM4909285	Human	Breast	IDC	1.77e-03	-2.09e-01	0.21
79083	MLPH	GSM4909286	Human	Breast	IDC	1.77e-06	-2.21e-01	0.1081
79083	MLPH	GSM4909290	Human	Breast	IDC	6.73e-03	1.72e-01	0.2096
79083	MLPH	GSM4909292	Human	Breast	IDC	1.49e-02	5.78e-01	0.1236
79083	MLPH	GSM4909293	Human	Breast	IDC	4.31e-24	5.05e-01	0.1581
79083	MLPH	GSM4909297	Human	Breast	IDC	5.74e-11	4.04e-01	0.1517
79083	MLPH	GSM4909298	Human	Breast	IDC	3.43e-35	6.86e-01	0.1551
79083	MLPH	GSM4909301	Human	Breast	IDC	2.52e-02	3.12e-01	0.1577
79083	MLPH	GSM4909302	Human	Breast	IDC	1.06e-07	3.91e-01	0.1545
79083	MLPH	GSM4909303	Human	Breast	IDC	6.39e-08	6.15e-01	0.0438
79083	MLPH	GSM4909304	Human	Breast	IDC	1.34e-14	4.84e-01	0.1636
79083	MLPH	GSM4909306	Human	Breast	IDC	2.97e-11	4.14e-01	0.1564
79083	MLPH	GSM4909308	Human	Breast	IDC	1.52e-08	2.38e-01	0.158
79083	MLPH	GSM4909311	Human	Breast	IDC	9.20e-08	2.75e-02	0.1534
79083	MLPH	GSM4909312	Human	Breast	IDC	3.49e-03	2.08e-01	0.1552
79083	MLPH	GSM4909313	Human	Breast	IDC	1.80e-07	4.45e-01	0.0391
79083	MLPH	GSM4909315	Human	Breast	IDC	8.99e-04	2.76e-01	0.21
79083	MLPH	GSM4909317	Human	Breast	IDC	6.02e-31	7.10e-01	0.1355
79083	MLPH	GSM4909318	Human	Breast	IDC	6.10e-06	6.80e-01	0.2031

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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
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:0051656	Colorectum	AD	establishment of organelle localization	131/3918	390/18723	3.00e-09	2.06e-07	131
GO:0051650	Colorectum	AD	establishment of vesicle localization	57/3918	161/18723	1.47e-05	3.15e-04	57
GO:0051648	Colorectum	AD	vesicle localization	59/3918	177/18723	7.83e-05	1.25e-03	59
GO:00516561	Colorectum	SER	establishment of organelle localization	100/2897	390/18723	1.11e-07	6.79e-06	100
GO:00516501	Colorectum	SER	establishment of vesicle localization	42/2897	161/18723	3.38e-04	5.35e-03	42
GO:00516481	Colorectum	SER	vesicle localization	43/2897	177/18723	1.41e-03	1.53e-02	43
GO:00516563	Colorectum	FAP	establishment of organelle localization	97/2622	390/18723	5.91e-09	9.48e-07	97
GO:00516503	Colorectum	FAP	establishment of vesicle localization	48/2622	161/18723	1.56e-07	9.64e-06	48
GO:00516483	Colorectum	FAP	vesicle localization	50/2622	177/18723	5.41e-07	2.72e-05	50
GO:00516564	Colorectum	CRC	establishment of organelle localization	76/2078	390/18723	6.53e-07	4.50e-05	76
GO:00516504	Colorectum	CRC	establishment of vesicle localization	39/2078	161/18723	1.82e-06	9.07e-05	39
GO:00516484	Colorectum	CRC	vesicle localization	41/2078	177/18723	3.39e-06	1.50e-04	41
GO:005165616	Esophagus	HGIN	establishment of organelle localization	90/2587	390/18723	4.27e-07	1.94e-05	90
GO:005165010	Esophagus	HGIN	establishment of vesicle localization	35/2587	161/18723	3.89e-03	3.54e-02	35
GO:005164810	Esophagus	HGIN	vesicle localization	37/2587	177/18723	6.03e-03	4.87e-02	37
GO:005165617	Esophagus	ESCC	establishment of organelle localization	273/8552	390/18723	9.13e-23	1.81e-20	273
GO:005165016	Esophagus	ESCC	establishment of vesicle localization	114/8552	161/18723	8.20e-11	2.53e-09	114
GO:005164815	Esophagus	ESCC	vesicle localization	119/8552	177/18723	5.16e-09	1.08e-07	119
GO:00330593	Esophagus	ESCC	cellular pigmentation	40/8552	53/18723	9.67e-06	9.21e-05	40
GO:00434731	Esophagus	ESCC	pigmentation	59/8552	98/18723	2.64e-03	1.12e-02	59

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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

MLPH

SNV

Missense_Mutation

rs371642307

c.592N>C

p.Glu198Gln

p.E198Q

Q9BV36

protein_coding

deleterious(0.02)

probably_damaging(0.981)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

MLPH

SNV

Missense_Mutation

c.943N>A

p.Asp315Asn

p.D315N

Q9BV36

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

MLPH

SNV

Missense_Mutation

c.404C>T

p.Ala135Val

p.A135V

Q9BV36

protein_coding

deleterious(0)

probably_damaging(0.973)

TCGA-BH-A18G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MLPH

SNV

Missense_Mutation

novel

c.894N>G

p.Ile298Met

p.I298M

Q9BV36

protein_coding

tolerated(0.22)

benign(0.143)

TCGA-C8-A8HQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MLPH

SNV

Missense_Mutation

c.943G>A

p.Asp315Asn

p.D315N

Q9BV36

protein_coding

deleterious(0)

probably_damaging(0.972)

TCGA-GM-A2D9-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

MLPH

SNV

Missense_Mutation

c.278N>A

p.Gly93Asp

p.G93D

Q9BV36

protein_coding

deleterious(0.02)

benign(0.372)

TCGA-GM-A2DH-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxol

MLPH

SNV

Missense_Mutation

novel

c.1045N>A

p.Ser349Thr

p.S349T

Q9BV36

protein_coding

tolerated(0.11)

benign(0.272)

TCGA-LL-A8F5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

MLPH

insertion

Frame_Shift_Ins

novel

c.784_785insAAGTG

p.Pro262GlnfsTer64

p.P262Qfs*64

Q9BV36

protein_coding

TCGA-AQ-A04J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MLPH

insertion

Frame_Shift_Ins

novel

c.785_786insCTGGAAAGCCTCAGGGCTTG

p.Thr263TrpfsTer68

p.T263Wfs*68

Q9BV36

protein_coding

TCGA-AQ-A04J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MLPH

SNV

Missense_Mutation

rs767964025

c.147N>C

p.Lys49Asn

p.K49N

Q9BV36

protein_coding

deleterious(0)

probably_damaging(0.944)

TCGA-EK-A2RJ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

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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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