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: LUC7L2

Gene summary for LUC7L2

Gene summary.

Gene information	Species	Human
	Gene symbol	LUC7L2
	Gene ID	51631
	Gene name	LUC7 like 2, pre-mRNA splicing factor
	Gene Alias	CGI-59
	Cytomap	7q34
	Gene Type	protein-coding
	GO ID	GO:0000245
	UniProtAcc	Q9Y383

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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
51631	LUC7L2	HTA11_3410_2000001011	Human	Colorectum	AD	1.38e-04	2.03e-01	0.0155
51631	LUC7L2	HTA11_2487_2000001011	Human	Colorectum	SER	5.13e-03	2.74e-01	-0.1808
51631	LUC7L2	HTA11_1938_2000001011	Human	Colorectum	AD	1.07e-12	5.90e-01	-0.0811
51631	LUC7L2	HTA11_78_2000001011	Human	Colorectum	AD	2.55e-26	9.41e-01	-0.1088
51631	LUC7L2	HTA11_347_2000001011	Human	Colorectum	AD	2.26e-45	1.04e+00	-0.1954
51631	LUC7L2	HTA11_411_2000001011	Human	Colorectum	SER	2.07e-02	7.30e-01	-0.2602
51631	LUC7L2	HTA11_83_2000001011	Human	Colorectum	SER	1.07e-08	5.98e-01	-0.1526
51631	LUC7L2	HTA11_696_2000001011	Human	Colorectum	AD	9.74e-15	5.98e-01	-0.1464
51631	LUC7L2	HTA11_866_2000001011	Human	Colorectum	AD	2.15e-15	5.88e-01	-0.1001
51631	LUC7L2	HTA11_1391_2000001011	Human	Colorectum	AD	1.39e-15	8.12e-01	-0.059
51631	LUC7L2	HTA11_7862_2000001011	Human	Colorectum	AD	5.26e-05	5.85e-01	-0.0179
51631	LUC7L2	HTA11_866_3004761011	Human	Colorectum	AD	3.42e-03	2.94e-01	0.096
51631	LUC7L2	HTA11_10623_2000001011	Human	Colorectum	AD	5.14e-05	6.12e-01	-0.0177
51631	LUC7L2	HTA11_6801_2000001011	Human	Colorectum	SER	3.71e-02	4.95e-01	0.0171
51631	LUC7L2	HTA11_10711_2000001011	Human	Colorectum	AD	2.26e-04	3.56e-01	0.0338
51631	LUC7L2	HTA11_7696_3000711011	Human	Colorectum	AD	1.53e-04	4.03e-01	0.0674
51631	LUC7L2	HTA11_6818_2000001011	Human	Colorectum	AD	6.12e-04	5.42e-01	0.0112
51631	LUC7L2	HTA11_6818_2000001021	Human	Colorectum	AD	4.75e-02	2.24e-01	0.0588
51631	LUC7L2	HTA11_99999970781_79442	Human	Colorectum	MSS	2.64e-16	7.09e-01	0.294
51631	LUC7L2	HTA11_99999965062_69753	Human	Colorectum	MSI-H	1.29e-03	8.62e-01	0.3487

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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
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
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:00718262	Colorectum	MSS	ribonucleoprotein complex subunit organization	90/3467	227/18723	6.88e-14	1.78e-11	90
GO:00226182	Colorectum	MSS	ribonucleoprotein complex assembly	88/3467	220/18723	7.12e-14	1.78e-11	88
GO:00226132	Colorectum	MSS	ribonucleoprotein complex biogenesis	144/3467	463/18723	2.76e-11	3.67e-09	144
GO:00002451	Colorectum	MSS	spliceosomal complex assembly	31/3467	79/18723	1.33e-05	3.07e-04	31
GO:00063761	Colorectum	MSS	mRNA splice site selection	17/3467	49/18723	5.28e-03	3.61e-02	17
GO:00226183	Colorectum	MSI-H	ribonucleoprotein complex assembly	62/1319	220/18723	7.13e-22	8.32e-19	62
GO:00718263	Colorectum	MSI-H	ribonucleoprotein complex subunit organization	63/1319	227/18723	8.08e-22	8.32e-19	63
GO:00226133	Colorectum	MSI-H	ribonucleoprotein complex biogenesis	95/1319	463/18723	1.04e-21	8.32e-19	95
GO:00083803	Colorectum	MSI-H	RNA splicing	82/1319	434/18723	1.22e-16	4.53e-14	82
GO:00003753	Colorectum	MSI-H	RNA splicing, via transesterification reactions	67/1319	324/18723	7.99e-16	2.61e-13	67
GO:00003773	Colorectum	MSI-H	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	66/1319	320/18723	1.51e-15	4.41e-13	66
GO:00003983	Colorectum	MSI-H	mRNA splicing, via spliceosome	66/1319	320/18723	1.51e-15	4.41e-13	66
GO:00002452	Colorectum	MSI-H	spliceosomal complex assembly	14/1319	79/18723	1.14e-03	1.90e-02	14
GO:00083804	Colorectum	FAP	RNA splicing	108/2622	434/18723	7.90e-10	1.86e-07	108
GO:00003754	Colorectum	FAP	RNA splicing, via transesterification reactions	84/2622	324/18723	8.06e-09	1.10e-06	84
GO:00003774	Colorectum	FAP	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	83/2622	320/18723	9.66e-09	1.23e-06	83
GO:00003984	Colorectum	FAP	mRNA splicing, via spliceosome	83/2622	320/18723	9.66e-09	1.23e-06	83
GO:00718264	Colorectum	FAP	ribonucleoprotein complex subunit organization	59/2622	227/18723	1.18e-06	5.26e-05	59
GO:00226184	Colorectum	FAP	ribonucleoprotein complex assembly	57/2622	220/18723	1.99e-06	8.03e-05	57
GO:00226134	Colorectum	FAP	ribonucleoprotein complex biogenesis	91/2622	463/18723	4.28e-04	5.12e-03	91

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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

LUC7L2

SNV

Missense_Mutation

novel

c.5N>T

p.Ser2Leu

p.S2L

Q9Y383

protein_coding

deleterious(0)

probably_damaging(0.963)

TCGA-5L-AAT1-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

letrozol

LUC7L2

SNV

Missense_Mutation

c.700N>A

p.Glu234Lys

p.E234K

Q9Y383

protein_coding

tolerated(0.19)

benign(0.025)

TCGA-A8-A06Q-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

LUC7L2

SNV

Missense_Mutation

c.935G>A

p.Arg312His

p.R312H

Q9Y383

protein_coding

tolerated_low_confidence(0.07)

probably_damaging(0.964)

TCGA-C8-A26V-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

LUC7L2

SNV

Missense_Mutation

c.705N>C

p.Lys235Asn

p.K235N

Q9Y383

protein_coding

deleterious(0.03)

probably_damaging(0.987)

TCGA-D8-A1JM-01

Breast

breast invasive carcinoma

Female

<65

I/II

ChemotherapyHormone Therapy

doxorubicine

LUC7L2

SNV

Missense_Mutation

rs761427902

c.899N>A

p.Arg300His

p.R300H

Q9Y383

protein_coding

tolerated_low_confidence(0.19)

probably_damaging(0.964)

TCGA-E2-A14T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

LUC7L2

SNV

Missense_Mutation

novel

c.488G>A

p.Arg163Gln

p.R163Q

Q9Y383

protein_coding

deleterious(0.02)

possibly_damaging(0.59)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

LUC7L2

SNV

Missense_Mutation

c.527C>A

p.Ser176Tyr

p.S176Y

Q9Y383

protein_coding

deleterious(0)

probably_damaging(0.969)

TCGA-A6-2675-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

LUC7L2

SNV

Missense_Mutation

rs754703629

c.1105C>T

p.Arg369Trp

p.R369W

Q9Y383

protein_coding

tolerated_low_confidence(0.15)

probably_damaging(0.973)

TCGA-AA-3867-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

LUC7L2

SNV

Missense_Mutation

rs761427902

c.899N>A

p.Arg300His

p.R300H

Q9Y383

protein_coding

tolerated_low_confidence(0.19)

probably_damaging(0.964)

TCGA-AD-6895-01

Colorectum

colon adenocarcinoma

Male

>=65

III/IV

Unknown

LUC7L2

SNV

Missense_Mutation

c.214G>A

p.Glu72Lys

p.E72K

Q9Y383

protein_coding

deleterious(0.02)

possibly_damaging(0.679)

TCGA-CA-6717-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Chemotherapy

oxaliplatin

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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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