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:003311921	Stomach	CSG	negative regulation of RNA splicing	7/1034	25/18723	3.07e-04	5.23e-03	7
GO:00975292	Stomach	CSG	myeloid leukocyte migration	25/1034	220/18723	5.03e-04	7.78e-03	25
GO:00716242	Stomach	CSG	positive regulation of granulocyte chemotaxis	7/1034	27/18723	5.14e-04	7.88e-03	7
GO:00975302	Stomach	CSG	granulocyte migration	19/1034	148/18723	5.21e-04	7.89e-03	19
GO:00096152	Stomach	CSG	response to virus	36/1034	367/18723	6.16e-04	8.96e-03	36
GO:19026242	Stomach	CSG	positive regulation of neutrophil migration	7/1034	28/18723	6.53e-04	9.33e-03	7
GO:00027642	Stomach	CSG	immune response-regulating signaling pathway	43/1034	468/18723	7.58e-04	1.04e-02	43
GO:000641721	Stomach	CSG	regulation of translation	43/1034	468/18723	7.58e-04	1.04e-02	43
GO:003052221	Stomach	CSG	intracellular receptor signaling pathway	28/1034	265/18723	7.73e-04	1.06e-02	28
GO:00603262	Stomach	CSG	cell chemotaxis	31/1034	310/18723	1.04e-03	1.33e-02	31
GO:000838011	Stomach	CSG	RNA splicing	40/1034	434/18723	1.07e-03	1.35e-02	40
GO:00026882	Stomach	CSG	regulation of leukocyte chemotaxis	16/1034	122/18723	1.11e-03	1.37e-02	16
GO:00716742	Stomach	CSG	mononuclear cell migration	22/1034	196/18723	1.25e-03	1.50e-02	22
GO:004348421	Stomach	CSG	regulation of RNA splicing	18/1034	148/18723	1.36e-03	1.58e-02	18
GO:00027532	Stomach	CSG	cytoplasmic pattern recognition receptor signaling pathway	10/1034	60/18723	1.53e-03	1.72e-02	10
GO:00305932	Stomach	CSG	neutrophil chemotaxis	14/1034	103/18723	1.57e-03	1.75e-02	14
GO:190002621	Stomach	CSG	positive regulation of substrate adhesion-dependent cell spreading	8/1034	41/18723	1.58e-03	1.76e-02	8
GO:00900232	Stomach	CSG	positive regulation of neutrophil chemotaxis	6/1034	24/18723	1.59e-03	1.76e-02	6
GO:00716222	Stomach	CSG	regulation of granulocyte chemotaxis	9/1034	51/18723	1.72e-03	1.88e-02	9
GO:000037711	Stomach	CSG	RNA splicing, via transesterification reactions with bulged adenosine as nucleophile	31/1034	320/18723	1.74e-03	1.89e-02	31

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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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