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: C1QBP

Gene summary for C1QBP

Gene summary.

Gene information	Species	Human
	Gene symbol	C1QBP
	Gene ID	708
	Gene name	complement C1q binding protein
	Gene Alias	COXPD33
	Cytomap	17p13.2
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	Q07021

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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
708	C1QBP	CA_HPV_1	Human	Cervix	CC	3.74e-07	-4.28e-02	0.0264
708	C1QBP	CA_HPV_3	Human	Cervix	CC	8.87e-06	2.87e-01	0.0414
708	C1QBP	CCI_1	Human	Cervix	CC	7.04e-07	-5.58e-01	0.528
708	C1QBP	CCI_3	Human	Cervix	CC	1.56e-08	-5.67e-01	0.516
708	C1QBP	CCII_1	Human	Cervix	CC	2.31e-17	-5.99e-01	0.3249
708	C1QBP	sample3	Human	Cervix	CC	1.83e-04	-2.28e-01	0.1387
708	C1QBP	H2	Human	Cervix	HSIL_HPV	8.49e-05	-3.09e-01	0.0632
708	C1QBP	L1	Human	Cervix	CC	7.87e-06	5.85e-02	0.0802
708	C1QBP	T3	Human	Cervix	CC	2.59e-06	-2.00e-01	0.1389
708	C1QBP	HTA11_347_2000001011	Human	Colorectum	AD	3.87e-05	2.40e-01	-0.1954
708	C1QBP	HTA11_696_2000001011	Human	Colorectum	AD	3.18e-03	2.08e-01	-0.1464
708	C1QBP	HTA11_866_2000001011	Human	Colorectum	AD	4.03e-03	1.64e-01	-0.1001
708	C1QBP	HTA11_1391_2000001011	Human	Colorectum	AD	8.19e-12	4.47e-01	-0.059
708	C1QBP	HTA11_866_3004761011	Human	Colorectum	AD	6.78e-09	4.33e-01	0.096
708	C1QBP	HTA11_4255_2000001011	Human	Colorectum	SER	5.15e-05	5.80e-01	0.0446
708	C1QBP	HTA11_7663_2000001011	Human	Colorectum	SER	6.93e-07	5.94e-01	0.0131
708	C1QBP	HTA11_6801_2000001011	Human	Colorectum	SER	9.83e-13	8.91e-01	0.0171
708	C1QBP	HTA11_7696_3000711011	Human	Colorectum	AD	3.47e-06	2.10e-01	0.0674
708	C1QBP	HTA11_99999970781_79442	Human	Colorectum	MSS	1.52e-18	4.87e-01	0.294
708	C1QBP	HTA11_99999965062_69753	Human	Colorectum	MSI-H	7.55e-07	1.07e+00	0.3487

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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
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
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:0050777	Liver	HCC	negative regulation of immune response	101/7958	194/18723	4.40e-03	1.90e-02	101
GO:00075651	Liver	HCC	female pregnancy	99/7958	193/18723	8.24e-03	3.23e-02	99
GO:0039530	Liver	HCC	MDA-5 signaling pathway	9/7958	11/18723	9.51e-03	3.60e-02	9
GO:0039532	Liver	HCC	negative regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway	9/7958	11/18723	9.51e-03	3.60e-02	9
GO:000166721	Liver	HCC	ameboidal-type cell migration	226/7958	475/18723	1.35e-02	4.81e-02	226
GO:002261320	Oral cavity	OSCC	ribonucleoprotein complex biogenesis	333/7305	463/18723	8.28e-48	5.24e-44	333
GO:000838020	Oral cavity	OSCC	RNA splicing	308/7305	434/18723	2.43e-42	7.70e-39	308
GO:004225420	Oral cavity	OSCC	ribosome biogenesis	230/7305	299/18723	3.22e-41	6.80e-38	230
GO:000037519	Oral cavity	OSCC	RNA splicing, via transesterification reactions	225/7305	324/18723	5.20e-29	2.99e-26	225
GO:000037719	Oral cavity	OSCC	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	221/7305	320/18723	5.50e-28	2.18e-25	221
GO:000039819	Oral cavity	OSCC	mRNA splicing, via spliceosome	221/7305	320/18723	5.50e-28	2.18e-25	221
GO:190331118	Oral cavity	OSCC	regulation of mRNA metabolic process	197/7305	288/18723	2.83e-24	7.16e-22	197
GO:005068417	Oral cavity	OSCC	regulation of mRNA processing	104/7305	137/18723	1.32e-18	1.58e-16	104
GO:000641720	Oral cavity	OSCC	regulation of translation	274/7305	468/18723	4.39e-18	4.63e-16	274
GO:004348420	Oral cavity	OSCC	regulation of RNA splicing	108/7305	148/18723	4.25e-17	3.69e-15	108
GO:004572719	Oral cavity	OSCC	positive regulation of translation	101/7305	136/18723	5.85e-17	4.94e-15	101
GO:003425019	Oral cavity	OSCC	positive regulation of cellular amide metabolic process	115/7305	162/18723	1.28e-16	1.05e-14	115
GO:000961515	Oral cavity	OSCC	response to virus	215/7305	367/18723	1.63e-14	9.41e-13	215
GO:01400533	Oral cavity	OSCC	mitochondrial gene expression	78/7305	108/18723	2.37e-12	9.86e-11	78
GO:004802420	Oral cavity	OSCC	regulation of mRNA splicing, via spliceosome	74/7305	101/18723	2.66e-12	1.09e-10	74

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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

C1QBP

SNV

Missense_Mutation

novel

c.529N>C

p.Asp177His

p.D177H

Q07021

protein_coding

tolerated(0.13)

possibly_damaging(0.807)

TCGA-HM-A4S6-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

C1QBP

SNV

Missense_Mutation

c.352N>A

p.Ala118Thr

p.A118T

Q07021

protein_coding

deleterious(0.04)

possibly_damaging(0.601)

TCGA-QG-A5Z2-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

C1QBP

SNV

Missense_Mutation

novel

c.304N>A

p.Leu102Ile

p.L102I

Q07021

protein_coding

tolerated(0.22)

possibly_damaging(0.562)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

C1QBP

SNV

Missense_Mutation

novel

c.814N>A

p.Leu272Ile

p.L272I

Q07021

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

C1QBP

SNV

Missense_Mutation

c.245N>C

p.Phe82Ser

p.F82S

Q07021

protein_coding

deleterious(0)

possibly_damaging(0.764)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

C1QBP

SNV

Missense_Mutation

rs115819590

c.643N>A

p.Gly215Ser

p.G215S

Q07021

protein_coding

tolerated_low_confidence(0.09)

benign(0.107)

TCGA-AP-A1DK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

C1QBP

SNV

Missense_Mutation

novel

c.751A>G

p.Thr251Ala

p.T251A

Q07021

protein_coding

tolerated(0.1)

possibly_damaging(0.559)

TCGA-D1-A175-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

paclitaxel

C1QBP

SNV

Missense_Mutation

novel

c.677N>C

p.Leu226Pro

p.L226P

Q07021

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-E6-A1LX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

C1QBP

SNV

Missense_Mutation

novel

c.296N>G

p.His99Arg

p.H99R

Q07021

protein_coding

tolerated(0.38)

benign(0.055)

TCGA-FI-A2D5-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

carboplatinum

C1QBP

SNV

Missense_Mutation

c.481N>A

p.Glu161Lys

p.E161K

Q07021

protein_coding

deleterious(0.02)

possibly_damaging(0.684)

TCGA-18-5595-01

Lung

lung squamous cell carcinoma

Male

<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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