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: MAP7

Gene summary for MAP7

Gene summary.

Gene information	Species	Human
	Gene symbol	MAP7
	Gene ID	9053
	Gene name	microtubule associated protein 7
	Gene Alias	E-MAP-115
	Cytomap	6q23.3
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	Q14244

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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
9053	MAP7	CCI_1	Human	Cervix	CC	8.69e-09	8.41e-01	0.528
9053	MAP7	CCI_2	Human	Cervix	CC	1.39e-06	8.50e-01	0.5249
9053	MAP7	CCI_3	Human	Cervix	CC	5.98e-09	7.39e-01	0.516
9053	MAP7	HTA11_3410_2000001011	Human	Colorectum	AD	3.74e-19	-6.07e-01	0.0155
9053	MAP7	HTA11_2487_2000001011	Human	Colorectum	SER	6.99e-06	-4.42e-01	-0.1808
9053	MAP7	HTA11_2951_2000001011	Human	Colorectum	AD	6.10e-09	-9.38e-01	0.0216
9053	MAP7	HTA11_347_2000001011	Human	Colorectum	AD	8.19e-07	5.75e-01	-0.1954
9053	MAP7	HTA11_411_2000001011	Human	Colorectum	SER	3.50e-04	6.02e-01	-0.2602
9053	MAP7	HTA11_5212_2000001011	Human	Colorectum	AD	1.61e-04	-5.34e-01	-0.2061
9053	MAP7	HTA11_5216_2000001011	Human	Colorectum	SER	7.98e-07	-5.69e-01	-0.1462
9053	MAP7	HTA11_7862_2000001011	Human	Colorectum	AD	1.96e-04	-3.48e-01	-0.0179
9053	MAP7	HTA11_8622_2000001021	Human	Colorectum	SER	2.71e-07	-5.09e-01	0.0528
9053	MAP7	HTA11_10711_2000001011	Human	Colorectum	AD	2.02e-02	-4.11e-01	0.0338
9053	MAP7	HTA11_7696_3000711011	Human	Colorectum	AD	2.53e-06	-4.18e-01	0.0674
9053	MAP7	HTA11_7469_2000001011	Human	Colorectum	AD	2.76e-04	-5.58e-01	-0.0124
9053	MAP7	HTA11_99999965062_69753	Human	Colorectum	MSI-H	7.74e-13	8.43e-01	0.3487
9053	MAP7	HTA11_99999965104_69814	Human	Colorectum	MSS	3.65e-07	5.57e-01	0.281
9053	MAP7	HTA11_99999973899_84307	Human	Colorectum	MSS	2.01e-09	-6.78e-01	0.2585
9053	MAP7	HTA11_99999974143_84620	Human	Colorectum	MSS	2.96e-17	-5.93e-01	0.3005
9053	MAP7	F007	Human	Colorectum	FAP	3.14e-03	-3.39e-01	0.1176

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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
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:0007163110	Skin	SCCIS	establishment or maintenance of cell polarity	31/919	218/18723	9.72e-08	1.29e-05	31
GO:0072659111	Skin	SCCIS	protein localization to plasma membrane	32/919	284/18723	1.07e-05	3.77e-04	32
GO:1990778110	Skin	SCCIS	protein localization to cell periphery	35/919	333/18723	1.93e-05	5.84e-04	35
GO:000697015	Skin	SCCIS	response to osmotic stress	11/919	84/18723	2.63e-03	2.48e-02	11
GO:000716327	Skin	cSCC	establishment or maintenance of cell polarity	103/4864	218/18723	9.44e-12	4.85e-10	103
GO:007265926	Skin	cSCC	protein localization to plasma membrane	118/4864	284/18723	6.43e-09	2.11e-07	118
GO:199077824	Skin	cSCC	protein localization to cell periphery	134/4864	333/18723	7.09e-09	2.30e-07	134
GO:000697021	Skin	cSCC	response to osmotic stress	35/4864	84/18723	1.23e-03	7.97e-03	35
GO:0072659112	Thyroid	PTC	protein localization to plasma membrane	153/5968	284/18723	9.90e-15	6.50e-13	153
GO:1990778111	Thyroid	PTC	protein localization to cell periphery	172/5968	333/18723	3.71e-14	2.30e-12	172
GO:0051258113	Thyroid	PTC	protein polymerization	154/5968	297/18723	5.35e-13	2.66e-11	154
GO:0007163111	Thyroid	PTC	establishment or maintenance of cell polarity	115/5968	218/18723	1.15e-10	3.90e-09	115
GO:00467858	Thyroid	PTC	microtubule polymerization	43/5968	83/18723	1.26e-04	9.98e-04	43
GO:00069709	Thyroid	PTC	response to osmotic stress	42/5968	84/18723	4.07e-04	2.73e-03	42
GO:00311096	Thyroid	PTC	microtubule polymerization or depolymerization	57/5968	122/18723	4.19e-04	2.81e-03	57
GO:007265928	Thyroid	ATC	protein localization to plasma membrane	161/6293	284/18723	8.45e-16	6.52e-14	161
GO:199077826	Thyroid	ATC	protein localization to cell periphery	181/6293	333/18723	3.72e-15	2.56e-13	181
GO:005125829	Thyroid	ATC	protein polymerization	159/6293	297/18723	9.33e-13	3.96e-11	159
GO:000716329	Thyroid	ATC	establishment or maintenance of cell polarity	122/6293	218/18723	8.46e-12	3.16e-10	122
GO:004678514	Thyroid	ATC	microtubule polymerization	45/6293	83/18723	8.75e-05	6.51e-04	45

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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

MAP7

SNV

Missense_Mutation

c.2154G>C

p.Gln718His

p.Q718H

protein_coding

deleterious(0)

possibly_damaging(0.824)

TCGA-3C-AALI-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Poly E

Complete Response

MAP7

SNV

Missense_Mutation

novel

c.1157C>T

p.Ala386Val

p.A386V

protein_coding

tolerated(0.23)

benign(0.395)

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MAP7

SNV

Missense_Mutation

c.2272G>A

p.Glu758Lys

p.E758K

protein_coding

tolerated(0.45)

benign(0.013)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MAP7

SNV

Missense_Mutation

novel

c.902G>A

p.Arg301Gln

p.R301Q

protein_coding

deleterious(0.02)

possibly_damaging(0.758)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MAP7

SNV

Missense_Mutation

c.1231N>C

p.Glu411Gln

p.E411Q

protein_coding

tolerated(0.12)

probably_damaging(0.986)

TCGA-D8-A1J8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

nolvadex

MAP7

insertion

Nonsense_Mutation

novel

c.1157_1158insATAATATTT

p.Ala386_Ala387insTer

p.A386_A387ins*

protein_coding

TCGA-A7-A0CJ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MAP7

deletion

Frame_Shift_Del

c.1283delN

p.Leu428GlnfsTer7

p.L428Qfs*7

protein_coding

TCGA-BH-A0B1-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

adriamycin

MAP7

SNV

Missense_Mutation

rs750272702

c.739G>A

p.Val247Ile

p.V247I

protein_coding

tolerated(1)

benign(0.341)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

MAP7

SNV

Missense_Mutation

novel

c.513N>C

p.Arg171Ser

p.R171S

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-C5-A1BQ-01

Cervix

cervical & endocervical cancer

Female

>=65

III/IV

Chemotherapy

cisplatin

MAP7

SNV

Missense_Mutation

rs755861106

c.448C>T

p.Arg150Trp

p.R150W

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-5M-AAT6-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

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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