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: CALR

Gene summary for CALR

Gene summary.

Gene information	Species	Human
	Gene symbol	CALR
	Gene ID	811
	Gene name	calreticulin
	Gene Alias	CRT
	Cytomap	19p13.13
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P27797

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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
811	CALR	GSM4909281	Human	Breast	IDC	2.73e-24	5.76e-01	0.21
811	CALR	GSM4909282	Human	Breast	IDC	7.36e-37	6.63e-01	-0.0288
811	CALR	GSM4909285	Human	Breast	IDC	8.17e-38	7.08e-01	0.21
811	CALR	GSM4909286	Human	Breast	IDC	1.46e-02	-2.26e-01	0.1081
811	CALR	GSM4909287	Human	Breast	IDC	5.96e-68	8.57e-01	0.2057
811	CALR	GSM4909288	Human	Breast	IDC	3.06e-04	8.18e-02	0.0988
811	CALR	GSM4909290	Human	Breast	IDC	1.13e-02	3.15e-01	0.2096
811	CALR	GSM4909292	Human	Breast	IDC	1.91e-05	5.77e-01	0.1236
811	CALR	GSM4909293	Human	Breast	IDC	1.19e-08	3.58e-01	0.1581
811	CALR	GSM4909294	Human	Breast	IDC	5.85e-11	-3.37e-01	0.2022
811	CALR	GSM4909296	Human	Breast	IDC	5.36e-10	-3.49e-02	0.1524
811	CALR	GSM4909297	Human	Breast	IDC	8.26e-27	8.44e-02	0.1517
811	CALR	GSM4909301	Human	Breast	IDC	1.82e-04	2.05e-01	0.1577
811	CALR	GSM4909304	Human	Breast	IDC	4.89e-10	4.05e-01	0.1636
811	CALR	GSM4909311	Human	Breast	IDC	2.57e-40	-1.29e-01	0.1534
811	CALR	GSM4909312	Human	Breast	IDC	9.40e-16	1.61e-01	0.1552
811	CALR	GSM4909313	Human	Breast	IDC	1.12e-03	-1.53e-01	0.0391
811	CALR	GSM4909316	Human	Breast	IDC	2.52e-04	-1.09e-01	0.21
811	CALR	GSM4909317	Human	Breast	IDC	3.83e-06	3.64e-01	0.1355
811	CALR	GSM4909318	Human	Breast	IDC	1.15e-04	-1.93e-02	0.2031

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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:00024749	Breast	Precancer	antigen processing and presentation of peptide antigen via MHC class I	7/1080	28/18723	8.46e-04	9.82e-03	7
GO:00305187	Breast	Precancer	intracellular steroid hormone receptor signaling pathway	16/1080	116/18723	1.01e-03	1.13e-02	16
GO:00716774	Breast	Precancer	positive regulation of mononuclear cell migration	11/1080	65/18723	1.13e-03	1.25e-02	11
GO:00075694	Breast	Precancer	cell aging	17/1080	132/18723	1.55e-03	1.59e-02	17
GO:19016549	Breast	Precancer	response to ketone	22/1080	194/18723	1.89e-03	1.84e-02	22
GO:19000268	Breast	Precancer	positive regulation of substrate adhesion-dependent cell spreading	8/1080	41/18723	2.08e-03	1.97e-02	8
GO:00026905	Breast	Precancer	positive regulation of leukocyte chemotaxis	13/1080	94/18723	2.83e-03	2.49e-02	13
GO:00025017	Breast	Precancer	peptide antigen assembly with MHC protein complex	5/1080	18/18723	2.88e-03	2.49e-02	5
GO:00305228	Breast	Precancer	intracellular receptor signaling pathway	27/1080	265/18723	2.99e-03	2.57e-02	27
GO:00509212	Breast	Precancer	positive regulation of chemotaxis	17/1080	141/18723	3.15e-03	2.65e-02	17
GO:00605374	Breast	Precancer	muscle tissue development	37/1080	403/18723	3.60e-03	2.98e-02	37
GO:00023967	Breast	Precancer	MHC protein complex assembly	5/1080	19/18723	3.73e-03	3.04e-02	5
GO:00108119	Breast	Precancer	positive regulation of cell-substrate adhesion	15/1080	123/18723	4.80e-03	3.64e-02	15
GO:19000248	Breast	Precancer	regulation of substrate adhesion-dependent cell spreading	9/1080	57/18723	5.04e-03	3.80e-02	9
GO:00509201	Breast	Precancer	regulation of chemotaxis	23/1080	223/18723	5.05e-03	3.80e-02	23
GO:00147063	Breast	Precancer	striated muscle tissue development	35/1080	384/18723	5.10e-03	3.83e-02	35
GO:00434018	Breast	Precancer	steroid hormone mediated signaling pathway	16/1080	136/18723	5.21e-03	3.88e-02	16
GO:0072503	Breast	Precancer	cellular divalent inorganic cation homeostasis	42/1080	486/18723	5.91e-03	4.21e-02	42
GO:00716754	Breast	Precancer	regulation of mononuclear cell migration	14/1080	115/18723	6.42e-03	4.48e-02	14
GO:00516047	Breast	Precancer	protein maturation	28/1080	294/18723	6.45e-03	4.50e-02	28

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0414118	Breast	Precancer	Protein processing in endoplasmic reticulum	33/684	174/8465	2.78e-06	3.83e-05	2.94e-05	33
hsa0461218	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa0516918	Breast	Precancer	Epstein-Barr virus infection	35/684	202/8465	1.15e-05	1.26e-04	9.64e-05	35
hsa0414518	Breast	Precancer	Phagosome	27/684	152/8465	7.37e-05	6.85e-04	5.25e-04	27
hsa0516618	Breast	Precancer	Human T-cell leukemia virus 1 infection	33/684	222/8465	4.29e-04	3.31e-03	2.53e-03	33
hsa0516316	Breast	Precancer	Human cytomegalovirus infection	32/684	225/8465	1.13e-03	7.57e-03	5.80e-03	32
hsa0414119	Breast	Precancer	Protein processing in endoplasmic reticulum	33/684	174/8465	2.78e-06	3.83e-05	2.94e-05	33
hsa0461219	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa0516919	Breast	Precancer	Epstein-Barr virus infection	35/684	202/8465	1.15e-05	1.26e-04	9.64e-05	35
hsa0414519	Breast	Precancer	Phagosome	27/684	152/8465	7.37e-05	6.85e-04	5.25e-04	27
hsa0516619	Breast	Precancer	Human T-cell leukemia virus 1 infection	33/684	222/8465	4.29e-04	3.31e-03	2.53e-03	33
hsa0516317	Breast	Precancer	Human cytomegalovirus infection	32/684	225/8465	1.13e-03	7.57e-03	5.80e-03	32
hsa0414522	Breast	IDC	Phagosome	34/867	152/8465	8.00e-06	9.99e-05	7.48e-05	34
hsa0516624	Breast	IDC	Human T-cell leukemia virus 1 infection	40/867	222/8465	2.52e-04	2.21e-03	1.66e-03	40
hsa0516324	Breast	IDC	Human cytomegalovirus infection	39/867	225/8465	6.66e-04	5.41e-03	4.05e-03	39
hsa0517014	Breast	IDC	Human immunodeficiency virus 1 infection	33/867	212/8465	9.28e-03	4.37e-02	3.27e-02	33
hsa0414532	Breast	IDC	Phagosome	34/867	152/8465	8.00e-06	9.99e-05	7.48e-05	34
hsa0516634	Breast	IDC	Human T-cell leukemia virus 1 infection	40/867	222/8465	2.52e-04	2.21e-03	1.66e-03	40
hsa0516334	Breast	IDC	Human cytomegalovirus infection	39/867	225/8465	6.66e-04	5.41e-03	4.05e-03	39
hsa0517015	Breast	IDC	Human immunodeficiency virus 1 infection	33/867	212/8465	9.28e-03	4.37e-02	3.27e-02	33

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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

CALR

insertion

Nonsense_Mutation

novel

c.1193_1194insCCAGATTCAAGCGATTCTCCTGCCTCGGCCTCCTGAGTAGCT

p.Glu398delinsAspGlnIleGlnAlaIleLeuLeuProArgProProGluTerLeu

p.E398delinsDQIQAILLPRPPE*L

P27797

protein_coding

TCGA-A2-A04Y-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CALR

SNV

Missense_Mutation

c.201N>C

p.Gln67His

p.Q67H

P27797

protein_coding

deleterious(0.01)

benign(0.254)

TCGA-IR-A3LK-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Chemotherapy

cisplatin

CALR

SNV

Missense_Mutation

c.1167N>T

p.Glu389Asp

p.E389D

P27797

protein_coding

tolerated(0.51)

benign(0)

TCGA-MY-A5BE-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

CALR

SNV

Missense_Mutation

c.298G>C

p.Glu100Gln

p.E100Q

P27797

protein_coding

deleterious(0.01)

benign(0.373)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

CALR

insertion

In_Frame_Ins

novel

c.1114_1115insTTGTCA

p.Glu372delinsValValLys

p.E372delinsVVK

P27797

protein_coding

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

CALR

SNV

Missense_Mutation

novel

c.308T>C

p.Ile103Thr

p.I103T

P27797

protein_coding

deleterious(0)

probably_damaging(0.984)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

CALR

SNV

Missense_Mutation

novel

c.193G>T

p.Gly65Cys

p.G65C

P27797

protein_coding

deleterious(0.01)

probably_damaging(1)

TCGA-AA-A010-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Chemotherapy

folinic

CALR

SNV

Missense_Mutation

c.667N>A

p.Ala223Thr

p.A223T

P27797

protein_coding

tolerated(0.38)

benign(0.228)

TCGA-CK-4951-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

CALR

SNV

Missense_Mutation

rs746740154

c.1231N>A

p.Gly411Ser

p.G411S

P27797

protein_coding

tolerated_low_confidence(0.57)

benign(0.039)

TCGA-CM-6162-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Chemotherapy

oxaliplatin

CALR

deletion

Frame_Shift_Del

c.791delC

p.Pro264GlnfsTer2

p.P264Qfs*2

P27797

protein_coding

TCGA-D5-6927-01

Colorectum

colon adenocarcinoma

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
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		RETINOIC ACID		9013706
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		OLTIPRAZ	OLTIPRAZ	15961673
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		GENTAMICIN	GENTAMICIN	15351734
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		GLUCOCORTICOID		8910610,8107808
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		ANTIANGIOGENIC		10498619
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		PEGINTERFERON ALFA-2A		26486786
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		Alpha 2 Interferon		26486786
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		VACCINIA VACCINE		15364449
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		RETINOID		9013706
811	CALR	EXTERNAL SIDE OF PLASMA MEMBRANE, CELL SURFACE, CLINICALLY ACTIONABLE, NUCLEAR HORMONE RECEPTOR, DRUGGABLE GENOME		N/A		26697989,25873496,26071474,26449662

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