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: C9orf78

Gene summary for C9ORF78

Gene summary.

Gene information	Species	Human
	Gene symbol	C9orf78
	Gene ID	51759
	Gene name	chromosome 9 open reading frame 78
	Gene Alias	CSU2
	Cytomap	9q34.11
	Gene Type	protein-coding
	GO ID	GO:0000375
	UniProtAcc	Q9NZ63

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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
51759	C9orf78	cirrhotic1	Human	Liver	Cirrhotic	2.94e-06	8.61e-02	0.0202
51759	C9orf78	cirrhotic2	Human	Liver	Cirrhotic	1.39e-09	1.26e-01	0.0201
51759	C9orf78	cirrhotic3	Human	Liver	Cirrhotic	1.28e-04	-2.36e-02	0.0215
51759	C9orf78	HCC1	Human	Liver	HCC	1.81e-17	5.37e+00	0.5336
51759	C9orf78	HCC2	Human	Liver	HCC	4.83e-20	5.06e+00	0.5341
51759	C9orf78	HCC5	Human	Liver	HCC	3.48e-04	2.35e+00	0.4932
51759	C9orf78	Pt13.b	Human	Liver	HCC	1.38e-12	-1.33e-03	0.0251
51759	C9orf78	S014	Human	Liver	HCC	4.79e-18	1.01e+00	0.2254
51759	C9orf78	S015	Human	Liver	HCC	3.59e-21	1.18e+00	0.2375
51759	C9orf78	S016	Human	Liver	HCC	1.67e-25	1.20e+00	0.2243
51759	C9orf78	S027	Human	Liver	HCC	1.95e-06	9.77e-01	0.2446
51759	C9orf78	S028	Human	Liver	HCC	3.97e-17	1.14e+00	0.2503
51759	C9orf78	S029	Human	Liver	HCC	3.11e-17	1.28e+00	0.2581
51759	C9orf78	C04	Human	Oral cavity	OSCC	2.64e-12	9.84e-01	0.2633
51759	C9orf78	C21	Human	Oral cavity	OSCC	1.80e-43	1.58e+00	0.2678
51759	C9orf78	C30	Human	Oral cavity	OSCC	1.54e-52	2.64e+00	0.3055
51759	C9orf78	C38	Human	Oral cavity	OSCC	6.49e-21	1.81e+00	0.172
51759	C9orf78	C43	Human	Oral cavity	OSCC	5.60e-46	9.01e-01	0.1704
51759	C9orf78	C46	Human	Oral cavity	OSCC	4.24e-40	1.07e+00	0.1673
51759	C9orf78	C51	Human	Oral cavity	OSCC	1.17e-12	9.46e-01	0.2674

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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
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:0008380	Colorectum	AD	RNA splicing	169/3918	434/18723	3.59e-18	2.04e-15	169
GO:0000377	Colorectum	AD	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000398	Colorectum	AD	mRNA splicing, via spliceosome	130/3918	320/18723	5.88e-16	2.16e-13	130
GO:0000375	Colorectum	AD	RNA splicing, via transesterification reactions	131/3918	324/18723	7.11e-16	2.22e-13	131
GO:00083802	Colorectum	MSS	RNA splicing	159/3467	434/18723	1.75e-19	1.22e-16	159
GO:00003772	Colorectum	MSS	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003982	Colorectum	MSS	mRNA splicing, via spliceosome	121/3467	320/18723	2.52e-16	8.27e-14	121
GO:00003752	Colorectum	MSS	RNA splicing, via transesterification reactions	122/3467	324/18723	2.75e-16	8.58e-14	122
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:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:0000375111	Esophagus	ESCC	RNA splicing, via transesterification reactions	248/8552	324/18723	3.05e-30	1.49e-27	248
GO:0000377111	Esophagus	ESCC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:0000398111	Esophagus	ESCC	mRNA splicing, via spliceosome	244/8552	320/18723	2.52e-29	1.07e-26	244
GO:000838012	Liver	Cirrhotic	RNA splicing	229/4634	434/18723	9.13e-37	2.86e-33	229
GO:000037512	Liver	Cirrhotic	RNA splicing, via transesterification reactions	175/4634	324/18723	5.95e-30	7.47e-27	175
GO:000037712	Liver	Cirrhotic	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	172/4634	320/18723	4.02e-29	3.60e-26	172
GO:000039812	Liver	Cirrhotic	mRNA splicing, via spliceosome	172/4634	320/18723	4.02e-29	3.60e-26	172

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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

C9orf78

SNV

Missense_Mutation

novel

c.855N>T

p.Met285Ile

p.M285I

Q9NZ63

protein_coding

tolerated(0.06)

benign(0.444)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

C9orf78

SNV

Missense_Mutation

novel

c.94N>C

p.Glu32Gln

p.E32Q

Q9NZ63

protein_coding

tolerated(0.06)

possibly_damaging(0.706)

TCGA-BH-A28O-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

C9orf78

insertion

Nonsense_Mutation

novel

c.704_705insAAATAAAAGCTACTCATAAGGTTAGCTGGGTGCAGT

p.Pro235_Ile236insAsnLysSerTyrSerTerGlyTerLeuGlyAlaVal

p.P235_I236insNKSYS*G*LGAV

Q9NZ63

protein_coding

TCGA-AN-A0FX-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

C9orf78

SNV

Missense_Mutation

c.97G>A

p.Glu33Lys

p.E33K

Q9NZ63

protein_coding

deleterious(0.01)

possibly_damaging(0.681)

TCGA-C5-A7UH-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

C9orf78

SNV

Missense_Mutation

novel

c.18G>T

p.Lys6Asn

p.K6N

Q9NZ63

protein_coding

deleterious(0.03)

benign(0.066)

TCGA-C5-A7UH-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

C9orf78

SNV

Missense_Mutation

rs139248631

c.701N>T

p.Ala234Val

p.A234V

Q9NZ63

protein_coding

tolerated(0.09)

benign(0.01)

TCGA-AA-A02R-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

C9orf78

SNV

Missense_Mutation

novel

c.415N>A

p.Pro139Thr

p.P139T

Q9NZ63

protein_coding

tolerated(0.52)

benign(0.038)

TCGA-AZ-4315-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

C9orf78

SNV

Missense_Mutation

novel

c.840N>T

p.Glu280Asp

p.E280D

Q9NZ63

protein_coding

tolerated(0.24)

benign(0.057)

TCGA-F5-6814-01

Colorectum

rectum adenocarcinoma

Male

<65

I/II

Unknown

C9orf78

insertion

Frame_Shift_Ins

novel

c.827_828insT

p.Tyr277LeufsTer4

p.Y277Lfs*4

Q9NZ63

protein_coding

TCGA-AA-3856-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

C9orf78

SNV

Missense_Mutation

rs758042858

c.700N>A

p.Ala234Thr

p.A234T

Q9NZ63

protein_coding

tolerated(0.22)

benign(0.001)

TCGA-AJ-A3OK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Chemotherapy

carboplatin

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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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