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: C7

Gene summary for C7

Gene summary.

Gene information	Species	Human
	Gene symbol	C7
	Gene ID	730
	Gene name	complement C7
	Gene Alias	C7
	Cytomap	5p13.1
	Gene Type	protein-coding
	GO ID	GO:0002250
	UniProtAcc	P10643

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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
730	C7	S41	Human	Liver	Cirrhotic	1.84e-05	9.56e-01	-0.0343
730	C7	S43	Human	Liver	Cirrhotic	8.05e-08	7.04e-01	-0.0187
730	C7	cirrhotic3	Human	Liver	Cirrhotic	3.02e-16	5.44e-01	0.0215
730	C7	HCC1	Human	Liver	HCC	4.11e-03	2.49e-01	0.5336

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Liver		HCC: Hepatocellular carcinoma
Liver		NAFLD: Non-alcoholic fatty liver disease

∗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:00481458	Esophagus	HGIN	regulation of fibroblast proliferation	23/2587	80/18723	3.71e-04	5.77e-03	23
GO:00000827	Esophagus	HGIN	G1/S transition of mitotic cell cycle	48/2587	214/18723	3.97e-04	6.07e-03	48
GO:00714265	Esophagus	HGIN	ribonucleoprotein complex export from nucleus	22/2587	76/18723	4.44e-04	6.62e-03	22
GO:001604919	Esophagus	HGIN	cell growth	93/2587	482/18723	4.49e-04	6.62e-03	93
GO:00481447	Esophagus	HGIN	fibroblast proliferation	23/2587	81/18723	4.52e-04	6.62e-03	23
GO:00327866	Esophagus	HGIN	positive regulation of DNA-templated transcription, elongation	11/2587	27/18723	5.28e-04	7.56e-03	11
GO:00448437	Esophagus	HGIN	cell cycle G1/S phase transition	52/2587	241/18723	6.19e-04	8.58e-03	52
GO:19028065	Esophagus	HGIN	regulation of cell cycle G1/S phase transition	39/2587	168/18723	6.60e-04	9.03e-03	39
GO:00329685	Esophagus	HGIN	positive regulation of transcription elongation from RNA polymerase II promoter	7/2587	13/18723	7.61e-04	1.00e-02	7
GO:00064056	Esophagus	HGIN	RNA export from nucleus	23/2587	84/18723	7.90e-04	1.03e-02	23
GO:20001343	Esophagus	HGIN	negative regulation of G1/S transition of mitotic cell cycle	23/2587	84/18723	7.90e-04	1.03e-02	23
GO:00709794	Esophagus	HGIN	protein K11-linked ubiquitination	11/2587	29/18723	1.08e-03	1.32e-02	11
GO:00311243	Esophagus	HGIN	mRNA 3'-end processing	18/2587	62/18723	1.37e-03	1.61e-02	18
GO:004390320	Esophagus	HGIN	regulation of biological process involved in symbiotic interaction	20/2587	72/18723	1.39e-03	1.63e-02	20
GO:003011116	Esophagus	HGIN	regulation of Wnt signaling pathway	65/2587	328/18723	1.53e-03	1.77e-02	65
GO:00327844	Esophagus	HGIN	regulation of DNA-templated transcription, elongation	16/2587	53/18723	1.58e-03	1.79e-02	16
GO:00459305	Esophagus	HGIN	negative regulation of mitotic cell cycle	49/2587	235/18723	1.88e-03	2.01e-02	49
GO:00063764	Esophagus	HGIN	mRNA splice site selection	15/2587	49/18723	1.88e-03	2.01e-02	15
GO:001605516	Esophagus	HGIN	Wnt signaling pathway	83/2587	444/18723	2.27e-03	2.33e-02	83
GO:19019915	Esophagus	HGIN	negative regulation of mitotic cell cycle phase transition	39/2587	179/18723	2.31e-03	2.36e-02	39

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0517122	Liver	Cirrhotic	Coronavirus disease - COVID-19	136/2530	232/8465	3.28e-20	1.82e-18	1.12e-18	136
hsa046102	Liver	Cirrhotic	Complement and coagulation cascades	48/2530	86/8465	4.41e-07	5.44e-06	3.35e-06	48
hsa0481021	Liver	Cirrhotic	Regulation of actin cytoskeleton	100/2530	229/8465	5.28e-06	5.50e-05	3.39e-05	100
hsa0517132	Liver	Cirrhotic	Coronavirus disease - COVID-19	136/2530	232/8465	3.28e-20	1.82e-18	1.12e-18	136
hsa046103	Liver	Cirrhotic	Complement and coagulation cascades	48/2530	86/8465	4.41e-07	5.44e-06	3.35e-06	48
hsa0481031	Liver	Cirrhotic	Regulation of actin cytoskeleton	100/2530	229/8465	5.28e-06	5.50e-05	3.39e-05	100
hsa0502022	Liver	HCC	Prion disease	195/4020	273/8465	3.26e-16	1.56e-14	8.67e-15	195
hsa0517142	Liver	HCC	Coronavirus disease - COVID-19	167/4020	232/8465	1.50e-14	4.19e-13	2.33e-13	167
hsa046104	Liver	HCC	Complement and coagulation cascades	57/4020	86/8465	3.19e-04	1.45e-03	8.04e-04	57
hsa0481041	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134
hsa0502032	Liver	HCC	Prion disease	195/4020	273/8465	3.26e-16	1.56e-14	8.67e-15	195
hsa0517152	Liver	HCC	Coronavirus disease - COVID-19	167/4020	232/8465	1.50e-14	4.19e-13	2.33e-13	167
hsa046105	Liver	HCC	Complement and coagulation cascades	57/4020	86/8465	3.19e-04	1.45e-03	8.04e-04	57
hsa0481051	Liver	HCC	Regulation of actin cytoskeleton	134/4020	229/8465	4.48e-04	1.94e-03	1.08e-03	134

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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

SNV

Missense_Mutation

c.2353N>C

p.Glu785Gln

p.E785Q

P10643

protein_coding

tolerated(1)

benign(0)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

SNV

Missense_Mutation

c.320C>T

p.Ser107Phe

p.S107F

P10643

protein_coding

tolerated(0.21)

possibly_damaging(0.77)

TCGA-AN-A0XW-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SNV

Missense_Mutation

rs376674018

c.148N>T

p.Arg50Trp

p.R50W

P10643

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-AO-A03T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SNV

Missense_Mutation

c.1639N>C

p.Asp547His

p.D547H

P10643

protein_coding

deleterious(0)

probably_damaging(0.966)

TCGA-C8-A12P-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SNV

Missense_Mutation

c.2037G>C

p.Trp679Cys

p.W679C

P10643

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D8-A1JK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SNV

Missense_Mutation

c.944T>C

p.Val315Ala

p.V315A

P10643

protein_coding

tolerated(0.31)

benign(0.207)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

SNV

Missense_Mutation

rs766182545

c.2353N>A

p.Glu785Lys

p.E785K

P10643

protein_coding

tolerated(0.07)

benign(0.003)

TCGA-D8-A27G-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SNV

Missense_Mutation

novel

c.2451N>T

p.Glu817Asp

p.E817D

P10643

protein_coding

deleterious(0.01)

probably_damaging(0.971)

TCGA-GI-A2C9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

insertion

Frame_Shift_Ins

novel

c.1744_1745insGCATTAATCAGTATCTCTTGACTGAGGAAGC

p.Val582GlyfsTer14

p.V582Gfs*14

P10643

protein_coding

TCGA-AN-A0FV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

insertion

In_Frame_Ins

novel

c.2350_2350+1insCTCTGA

p.Ala784_Glu785insLeuThr

p.A784_E785insLT

P10643

protein_coding

TCGA-AR-A0U0-01

Breast

breast invasive 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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