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: MID1

Gene summary for MID1

Gene summary.

Gene information	Species	Human
	Gene symbol	MID1
	Gene ID	4281
	Gene name	midline 1
	Gene Alias	BBBG1
	Cytomap	Xp22.2
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	A0A024RBV4

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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
4281	MID1	RNA-P3T-P3T-4	Human	Lung	IAC	4.71e-04	5.42e-01	0.1859
4281	MID1	RNA-P6T2-P6T2-1	Human	Lung	IAC	1.90e-33	9.33e-01	-0.0166
4281	MID1	RNA-P6T2-P6T2-2	Human	Lung	IAC	2.86e-36	9.45e-01	-0.0132
4281	MID1	RNA-P6T2-P6T2-3	Human	Lung	IAC	3.51e-37	9.76e-01	-0.013
4281	MID1	RNA-P6T2-P6T2-4	Human	Lung	IAC	4.90e-33	9.58e-01	-0.0121
4281	MID1	RNA-P7T1-P7T1-1	Human	Lung	AIS	2.25e-02	5.49e-01	-0.0961
4281	MID1	RNA-P7T1-P7T1-2	Human	Lung	AIS	2.12e-06	6.71e-01	-0.0876
4281	MID1	RNA-P7T1-P7T1-4	Human	Lung	AIS	1.01e-03	5.04e-01	-0.0809
4281	MID1	C30	Human	Oral cavity	OSCC	2.34e-13	6.57e-01	0.3055
4281	MID1	C43	Human	Oral cavity	OSCC	3.44e-22	4.80e-01	0.1704
4281	MID1	C46	Human	Oral cavity	OSCC	3.39e-05	1.50e-01	0.1673
4281	MID1	C51	Human	Oral cavity	OSCC	2.42e-06	4.64e-01	0.2674
4281	MID1	LN22	Human	Oral cavity	OSCC	4.81e-02	6.92e-01	0.1733
4281	MID1	NEOLP-1	Human	Oral cavity	NEOLP	2.41e-08	3.56e-01	-0.0194
4281	MID1	SYSMH1	Human	Oral cavity	OSCC	4.79e-10	2.82e-01	0.1127
4281	MID1	SYSMH2	Human	Oral cavity	OSCC	2.49e-05	1.78e-01	0.2326
4281	MID1	SYSMH3	Human	Oral cavity	OSCC	6.06e-13	3.04e-01	0.2442
4281	MID1	SYSMH4	Human	Oral cavity	OSCC	5.80e-08	5.68e-02	0.1226

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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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma

∗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:190290310	Cervix	CC	regulation of supramolecular fiber organization	92/2311	383/18723	1.49e-10	2.48e-08	92
GO:00310988	Cervix	CC	stress-activated protein kinase signaling cascade	58/2311	247/18723	8.02e-07	2.89e-05	58
GO:00514038	Cervix	CC	stress-activated MAPK cascade	55/2311	239/18723	2.96e-06	8.31e-05	55
GO:00703027	Cervix	CC	regulation of stress-activated protein kinase signaling cascade	46/2311	195/18723	9.35e-06	2.11e-04	46
GO:19029048	Cervix	CC	negative regulation of supramolecular fiber organization	40/2311	167/18723	2.39e-05	4.17e-04	40
GO:00434104	Cervix	CC	positive regulation of MAPK cascade	90/2311	480/18723	2.92e-05	4.83e-04	90
GO:00328727	Cervix	CC	regulation of stress-activated MAPK cascade	44/2311	192/18723	3.09e-05	5.10e-04	44
GO:002241110	Cervix	CC	cellular component disassembly	83/2311	443/18723	6.04e-05	8.68e-04	83
GO:00106399	Cervix	CC	negative regulation of organelle organization	68/2311	348/18723	7.40e-05	1.03e-03	68
GO:00514948	Cervix	CC	negative regulation of cytoskeleton organization	37/2311	163/18723	1.57e-04	1.88e-03	37
GO:00705074	Cervix	CC	regulation of microtubule cytoskeleton organization	32/2311	148/18723	1.02e-03	8.51e-03	32
GO:00703043	Cervix	CC	positive regulation of stress-activated protein kinase signaling cascade	27/2311	128/18723	3.49e-03	2.26e-02	27
GO:00329847	Cervix	CC	protein-containing complex disassembly	41/2311	224/18723	6.13e-03	3.48e-02	41
GO:0031111	Cervix	CC	negative regulation of microtubule polymerization or depolymerization	11/2311	40/18723	7.54e-03	4.02e-02	11
GO:00311101	Cervix	CC	regulation of microtubule polymerization or depolymerization	19/2311	88/18723	1.01e-02	4.91e-02	19
GO:1902903	Colorectum	AD	regulation of supramolecular fiber organization	139/3918	383/18723	2.01e-12	3.19e-10	139
GO:0022411	Colorectum	AD	cellular component disassembly	147/3918	443/18723	8.53e-10	6.76e-08	147
GO:0032984	Colorectum	AD	protein-containing complex disassembly	81/3918	224/18723	9.41e-08	4.65e-06	81
GO:0010639	Colorectum	AD	negative regulation of organelle organization	114/3918	348/18723	1.41e-07	6.49e-06	114
GO:1902904	Colorectum	AD	negative regulation of supramolecular fiber organization	60/3918	167/18723	5.23e-06	1.35e-04	60

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0412014	Cervix	CC	Ubiquitin mediated proteolysis	49/1267	142/8465	4.26e-09	7.68e-08	4.54e-08	49
hsa0412015	Cervix	CC	Ubiquitin mediated proteolysis	49/1267	142/8465	4.26e-09	7.68e-08	4.54e-08	49
hsa04120	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041201	Colorectum	AD	Ubiquitin mediated proteolysis	58/2092	142/8465	1.46e-05	1.53e-04	9.76e-05	58
hsa041202	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041203	Colorectum	SER	Ubiquitin mediated proteolysis	39/1580	142/8465	6.18e-03	3.66e-02	2.66e-02	39
hsa041204	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa041205	Colorectum	MSS	Ubiquitin mediated proteolysis	55/1875	142/8465	5.02e-06	6.00e-05	3.68e-05	55
hsa041206	Colorectum	FAP	Ubiquitin mediated proteolysis	51/1404	142/8465	1.55e-08	5.84e-07	3.55e-07	51
hsa041207	Colorectum	FAP	Ubiquitin mediated proteolysis	51/1404	142/8465	1.55e-08	5.84e-07	3.55e-07	51
hsa041208	Colorectum	CRC	Ubiquitin mediated proteolysis	42/1091	142/8465	9.98e-08	6.67e-06	4.52e-06	42
hsa041209	Colorectum	CRC	Ubiquitin mediated proteolysis	42/1091	142/8465	9.98e-08	6.67e-06	4.52e-06	42
hsa0412016	Endometrium	AEH	Ubiquitin mediated proteolysis	41/1197	142/8465	3.42e-06	4.27e-05	3.13e-05	41
hsa0412017	Endometrium	AEH	Ubiquitin mediated proteolysis	41/1197	142/8465	3.42e-06	4.27e-05	3.13e-05	41
hsa0412023	Endometrium	EEC	Ubiquitin mediated proteolysis	41/1237	142/8465	7.86e-06	9.58e-05	7.14e-05	41
hsa0412033	Endometrium	EEC	Ubiquitin mediated proteolysis	41/1237	142/8465	7.86e-06	9.58e-05	7.14e-05	41
hsa0412026	Esophagus	HGIN	Ubiquitin mediated proteolysis	49/1383	142/8465	7.78e-08	1.33e-06	1.06e-06	49
hsa04120111	Esophagus	HGIN	Ubiquitin mediated proteolysis	49/1383	142/8465	7.78e-08	1.33e-06	1.06e-06	49
hsa0412027	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122
hsa0412036	Esophagus	ESCC	Ubiquitin mediated proteolysis	122/4205	142/8465	6.53e-20	7.29e-18	3.74e-18	122

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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

MID1

SNV

Missense_Mutation

c.427N>A

p.Asp143Asn

p.D143N

O15344

protein_coding

tolerated(0.22)

benign(0.025)

TCGA-A2-A0CL-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

MID1

SNV

Missense_Mutation

c.265N>A

p.Ala89Thr

p.A89T

O15344

protein_coding

deleterious(0.01)

possibly_damaging(0.602)

TCGA-A8-A07W-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

exemestane

MID1

SNV

Missense_Mutation

novel

c.1825N>A

p.Asp609Asn

p.D609N

O15344

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A08H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MID1

SNV

Missense_Mutation

rs150291968

c.1888G>A

p.Asp630Asn

p.D630N

O15344

protein_coding

tolerated(0.18)

benign(0.009)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MID1

SNV

Missense_Mutation

c.224N>A

p.Arg75His

p.R75H

O15344

protein_coding

deleterious(0)

probably_damaging(0.981)

TCGA-B6-A40B-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MID1

SNV

Missense_Mutation

rs765748631

c.203N>A

p.Arg68Gln

p.R68Q

O15344

protein_coding

deleterious(0.01)

benign(0.06)

TCGA-BH-A0B6-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MID1

SNV

Missense_Mutation

c.616N>A

p.Asp206Asn

p.D206N

O15344

protein_coding

tolerated(0.3)

benign(0.07)

TCGA-BH-A0C1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

MID1

SNV

Missense_Mutation

c.1082C>T

p.Thr361Ile

p.T361I

O15344

protein_coding

tolerated(0.05)

benign(0.093)

TCGA-E9-A1N9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

MID1

SNV

Missense_Mutation

c.712N>C

p.Glu238Gln

p.E238Q

O15344

protein_coding

tolerated(0.24)

benign(0.146)

TCGA-E9-A1RG-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

MID1

SNV

Missense_Mutation

c.373N>A

p.Asp125Asn

p.D125N

O15344

protein_coding

deleterious(0.03)

benign(0.052)

TCGA-GM-A2DN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxol

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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
4281	MID1	ENZYME, B30_2 SPRY DOMAIN, DRUGGABLE GENOME		SUN-N8075

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