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: LUC7L

Gene summary for LUC7L

Gene summary.

Gene information	Species	Human
	Gene symbol	LUC7L
	Gene ID	55692
	Gene name	LUC7 like
	Gene Alias	LUC7B1
	Cytomap	16p13.3
	Gene Type	protein-coding
	GO ID	GO:0000245
	UniProtAcc	Q1W6G4

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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
55692	LUC7L	HTA11_3410_2000001011	Human	Colorectum	AD	1.00e-02	-3.25e-01	0.0155
55692	LUC7L	A015-C-203	Human	Colorectum	FAP	1.87e-22	1.94e-01	-0.1294
55692	LUC7L	A015-C-204	Human	Colorectum	FAP	3.02e-02	2.22e-01	-0.0228
55692	LUC7L	A002-C-201	Human	Colorectum	FAP	1.85e-07	1.51e-01	0.0324
55692	LUC7L	A001-C-119	Human	Colorectum	FAP	1.20e-16	6.63e-01	-0.1557
55692	LUC7L	A001-C-108	Human	Colorectum	FAP	5.02e-15	2.76e-01	-0.0272
55692	LUC7L	A002-C-205	Human	Colorectum	FAP	2.14e-19	3.08e-01	-0.1236
55692	LUC7L	A001-C-104	Human	Colorectum	FAP	2.57e-07	3.21e-01	0.0184
55692	LUC7L	A015-C-006	Human	Colorectum	FAP	2.78e-12	2.99e-01	-0.0994
55692	LUC7L	A015-C-106	Human	Colorectum	FAP	1.03e-08	1.06e-01	-0.0511
55692	LUC7L	A002-C-114	Human	Colorectum	FAP	1.64e-11	1.77e-01	-0.1561
55692	LUC7L	A015-C-104	Human	Colorectum	FAP	3.89e-26	2.74e-01	-0.1899
55692	LUC7L	A001-C-014	Human	Colorectum	FAP	3.66e-09	1.59e-01	0.0135
55692	LUC7L	A002-C-016	Human	Colorectum	FAP	1.70e-13	8.73e-02	0.0521
55692	LUC7L	A015-C-002	Human	Colorectum	FAP	2.37e-05	5.51e-02	-0.0763
55692	LUC7L	A001-C-203	Human	Colorectum	FAP	2.75e-07	1.50e-01	-0.0481
55692	LUC7L	A002-C-116	Human	Colorectum	FAP	9.86e-24	8.67e-02	-0.0452
55692	LUC7L	A014-C-008	Human	Colorectum	FAP	5.08e-09	1.46e-01	-0.191
55692	LUC7L	A018-E-020	Human	Colorectum	FAP	7.04e-14	2.26e-01	-0.2034
55692	LUC7L	F034	Human	Colorectum	FAP	1.36e-17	2.54e-01	-0.0665

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
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:00226139	Breast	Precancer	ribonucleoprotein complex biogenesis	79/1080	463/18723	2.11e-18	1.03e-15	79
GO:00718269	Breast	Precancer	ribonucleoprotein complex subunit organization	48/1080	227/18723	2.68e-15	8.45e-13	48
GO:00226189	Breast	Precancer	ribonucleoprotein complex assembly	47/1080	220/18723	3.47e-15	1.03e-12	47
GO:00083809	Breast	Precancer	RNA splicing	65/1080	434/18723	1.27e-12	2.53e-10	65
GO:00003759	Breast	Precancer	RNA splicing, via transesterification reactions	52/1080	324/18723	1.74e-11	2.22e-09	52
GO:00003779	Breast	Precancer	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	51/1080	320/18723	3.55e-11	4.04e-09	51
GO:00003989	Breast	Precancer	mRNA splicing, via spliceosome	51/1080	320/18723	3.55e-11	4.04e-09	51
GO:002261314	Breast	IDC	ribonucleoprotein complex biogenesis	83/1434	463/18723	2.01e-13	5.20e-11	83
GO:007182614	Breast	IDC	ribonucleoprotein complex subunit organization	52/1434	227/18723	5.18e-13	1.21e-10	52
GO:002261814	Breast	IDC	ribonucleoprotein complex assembly	51/1434	220/18723	5.32e-13	1.21e-10	51
GO:000838014	Breast	IDC	RNA splicing	73/1434	434/18723	1.27e-10	1.57e-08	73
GO:000037514	Breast	IDC	RNA splicing, via transesterification reactions	58/1434	324/18723	9.44e-10	9.58e-08	58
GO:000037714	Breast	IDC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	57/1434	320/18723	1.60e-09	1.49e-07	57
GO:000039814	Breast	IDC	mRNA splicing, via spliceosome	57/1434	320/18723	1.60e-09	1.49e-07	57
GO:002261324	Breast	DCIS	ribonucleoprotein complex biogenesis	83/1390	463/18723	3.65e-14	1.09e-11	83
GO:007182624	Breast	DCIS	ribonucleoprotein complex subunit organization	52/1390	227/18723	1.54e-13	3.95e-11	52
GO:002261824	Breast	DCIS	ribonucleoprotein complex assembly	51/1390	220/18723	1.60e-13	3.95e-11	51
GO:000838024	Breast	DCIS	RNA splicing	73/1390	434/18723	3.05e-11	5.08e-09	73
GO:000037524	Breast	DCIS	RNA splicing, via transesterification reactions	58/1390	324/18723	2.89e-10	3.34e-08	58
GO:000037724	Breast	DCIS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	57/1390	320/18723	5.01e-10	5.35e-08	57

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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

LUC7L

insertion

In_Frame_Ins

novel

c.414_415insGGCCAGCTATGGTGGCTCTTGGCTTTAGTCTCAGCTGTTCGGGAG

p.Ala138_Lys139insGlyGlnLeuTrpTrpLeuLeuAlaLeuValSerAlaValArgGlu

p.A138_K139insGQLWWLLALVSAVRE

Q9NQ29

protein_coding

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

LUC7L

SNV

Missense_Mutation

rs770266344

c.965C>T

p.Ala322Val

p.A322V

Q9NQ29

protein_coding

deleterious_low_confidence(0.01)

benign(0.022)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

LUC7L

SNV

Missense_Mutation

novel

c.454T>C

p.Ser152Pro

p.S152P

Q9NQ29

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

LUC7L

SNV

Missense_Mutation

c.740N>C

p.Arg247Thr

p.R247T

Q9NQ29

protein_coding

deleterious(0.03)

benign(0.432)

TCGA-JX-A3Q0-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

LUC7L

SNV

Missense_Mutation

c.740N>C

p.Arg247Thr

p.R247T

Q9NQ29

protein_coding

deleterious(0.03)

benign(0.432)

TCGA-UC-A7PG-06

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

LUC7L

SNV

Missense_Mutation

c.71N>A

p.Thr24Asn

p.T24N

Q9NQ29

protein_coding

tolerated(0.31)

benign(0.03)

TCGA-AA-3815-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

LUC7L

SNV

Missense_Mutation

rs764753668

c.1021N>T

p.Arg341Trp

p.R341W

Q9NQ29

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.451)

TCGA-CK-5913-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

LUC7L

SNV

Missense_Mutation

novel

c.260N>A

p.Met87Lys

p.M87K

Q9NQ29

protein_coding

deleterious(0)

possibly_damaging(0.484)

TCGA-AG-A01N-01

Colorectum

rectum adenocarcinoma

Female

>=65

III/IV

Chemotherapy

capecitabine

LUC7L

SNV

Missense_Mutation

rs772200033

c.811N>T

p.Arg271Cys

p.R271C

Q9NQ29

protein_coding

deleterious(0.03)

probably_damaging(0.982)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

LUC7L

SNV

Missense_Mutation

novel

c.611N>A

p.Arg204His

p.R204H

Q9NQ29

protein_coding

deleterious(0)

possibly_damaging(0.581)

TCGA-A5-A1OF-01

Endometrium

uterine corpus endometrioid carcinoma

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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