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: HSPA5

Gene summary for HSPA5

Gene summary.

Gene information	Species	Human
	Gene symbol	HSPA5
	Gene ID	3309
	Gene name	heat shock protein family A (Hsp70) member 5
	Gene Alias	BIP
	Cytomap	9q33.3
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	P11021

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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
3309	HSPA5	GSM4909282	Human	Breast	IDC	1.49e-02	-3.95e-01	-0.0288
3309	HSPA5	GSM4909285	Human	Breast	IDC	1.29e-02	1.30e-01	0.21
3309	HSPA5	GSM4909286	Human	Breast	IDC	5.38e-21	-6.23e-01	0.1081
3309	HSPA5	GSM4909287	Human	Breast	IDC	3.36e-07	3.56e-01	0.2057
3309	HSPA5	GSM4909290	Human	Breast	IDC	8.51e-08	-4.22e-01	0.2096
3309	HSPA5	GSM4909293	Human	Breast	IDC	5.55e-03	-4.45e-02	0.1581
3309	HSPA5	GSM4909294	Human	Breast	IDC	1.49e-09	-4.84e-01	0.2022
3309	HSPA5	GSM4909296	Human	Breast	IDC	7.65e-10	-4.23e-01	0.1524
3309	HSPA5	GSM4909297	Human	Breast	IDC	1.26e-09	-3.70e-01	0.1517
3309	HSPA5	GSM4909298	Human	Breast	IDC	3.65e-11	-4.26e-01	0.1551
3309	HSPA5	GSM4909302	Human	Breast	IDC	3.52e-14	-5.10e-01	0.1545
3309	HSPA5	GSM4909304	Human	Breast	IDC	1.89e-03	-3.23e-01	0.1636
3309	HSPA5	GSM4909305	Human	Breast	IDC	3.39e-04	-3.44e-01	0.0436
3309	HSPA5	GSM4909306	Human	Breast	IDC	2.41e-09	-5.12e-01	0.1564
3309	HSPA5	GSM4909307	Human	Breast	IDC	4.78e-16	-6.13e-01	0.1569
3309	HSPA5	GSM4909308	Human	Breast	IDC	4.57e-12	-4.90e-01	0.158
3309	HSPA5	GSM4909309	Human	Breast	IDC	2.73e-18	-5.98e-01	0.0483
3309	HSPA5	GSM4909311	Human	Breast	IDC	1.51e-23	-5.13e-01	0.1534
3309	HSPA5	GSM4909312	Human	Breast	IDC	2.80e-09	-3.82e-01	0.1552
3309	HSPA5	GSM4909313	Human	Breast	IDC	1.01e-10	-4.32e-01	0.0391

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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
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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:00713537	Thyroid	HT	cellular response to interleukin-4	7/1272	33/18723	5.88e-03	3.74e-02	7
GO:005159218	Thyroid	HT	response to calcium ion	19/1272	149/18723	5.92e-03	3.76e-02	19
GO:00170158	Thyroid	HT	regulation of transforming growth factor beta receptor signaling pathway	17/1272	128/18723	5.97e-03	3.77e-02	17
GO:00084064	Thyroid	HT	gonad development	25/1272	221/18723	8.46e-03	4.82e-02	25
GO:0010498113	Thyroid	PTC	proteasomal protein catabolic process	297/5968	490/18723	4.58e-40	9.63e-37	297
GO:0043161113	Thyroid	PTC	proteasome-mediated ubiquitin-dependent protein catabolic process	254/5968	412/18723	3.91e-36	4.54e-33	254
GO:0072594112	Thyroid	PTC	establishment of protein localization to organelle	244/5968	422/18723	1.18e-28	4.97e-26	244
GO:0034976113	Thyroid	PTC	response to endoplasmic reticulum stress	161/5968	256/18723	1.14e-24	3.27e-22	161
GO:0006457112	Thyroid	PTC	protein folding	137/5968	212/18723	8.29e-23	2.01e-20	137
GO:1903320113	Thyroid	PTC	regulation of protein modification by small protein conjugation or removal	148/5968	242/18723	4.49e-21	8.10e-19	148
GO:0006605113	Thyroid	PTC	protein targeting	180/5968	314/18723	6.81e-21	1.19e-18	180
GO:0031396113	Thyroid	PTC	regulation of protein ubiquitination	128/5968	210/18723	3.06e-18	3.27e-16	128
GO:0090150112	Thyroid	PTC	establishment of protein localization to membrane	149/5968	260/18723	1.64e-17	1.59e-15	149
GO:0035966113	Thyroid	PTC	response to topologically incorrect protein	101/5968	159/18723	2.00e-16	1.66e-14	101
GO:0043254113	Thyroid	PTC	regulation of protein-containing complex assembly	215/5968	428/18723	1.23e-15	9.09e-14	215
GO:0006986113	Thyroid	PTC	response to unfolded protein	87/5968	137/18723	2.46e-14	1.57e-12	87
GO:00365038	Thyroid	PTC	ERAD pathway	71/5968	107/18723	2.37e-13	1.22e-11	71
GO:0045185113	Thyroid	PTC	maintenance of protein location	64/5968	94/18723	5.92e-13	2.85e-11	64
GO:003043315	Thyroid	PTC	ubiquitin-dependent ERAD pathway	59/5968	85/18723	1.30e-12	5.91e-11	59
GO:0035967113	Thyroid	PTC	cellular response to topologically incorrect protein	73/5968	116/18723	5.62e-12	2.41e-10	73

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0501218	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502016	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501416	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502216	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0414118	Breast	Precancer	Protein processing in endoplasmic reticulum	33/684	174/8465	2.78e-06	3.83e-05	2.94e-05	33
hsa0541718	Breast	Precancer	Lipid and atherosclerosis	37/684	215/8465	7.64e-06	9.29e-05	7.12e-05	37
hsa0461218	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa030609	Breast	Precancer	Protein export	6/684	23/8465	8.34e-03	4.54e-02	3.48e-02	6
hsa0501219	Breast	Precancer	Parkinson disease	99/684	266/8465	3.58e-42	5.65e-40	4.33e-40	99
hsa0502017	Breast	Precancer	Prion disease	95/684	273/8465	1.39e-37	1.46e-35	1.12e-35	95
hsa0501417	Breast	Precancer	Amyotrophic lateral sclerosis	98/684	364/8465	2.13e-28	8.41e-27	6.44e-27	98
hsa0502217	Breast	Precancer	Pathways of neurodegeneration - multiple diseases	112/684	476/8465	6.96e-27	2.44e-25	1.87e-25	112
hsa0414119	Breast	Precancer	Protein processing in endoplasmic reticulum	33/684	174/8465	2.78e-06	3.83e-05	2.94e-05	33
hsa0541719	Breast	Precancer	Lipid and atherosclerosis	37/684	215/8465	7.64e-06	9.29e-05	7.12e-05	37
hsa0461219	Breast	Precancer	Antigen processing and presentation	19/684	78/8465	9.61e-06	1.12e-04	8.62e-05	19
hsa0306012	Breast	Precancer	Protein export	6/684	23/8465	8.34e-03	4.54e-02	3.48e-02	6
hsa0501224	Breast	IDC	Parkinson disease	107/867	266/8465	2.57e-39	8.36e-37	6.26e-37	107
hsa0502023	Breast	IDC	Prion disease	102/867	273/8465	3.70e-34	4.01e-32	3.00e-32	102
hsa0501423	Breast	IDC	Amyotrophic lateral sclerosis	102/867	364/8465	1.29e-22	5.22e-21	3.91e-21	102
hsa0502223	Breast	IDC	Pathways of neurodegeneration - multiple diseases	116/867	476/8465	3.63e-20	1.18e-18	8.82e-19	116

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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

HSPA5

SNV

Missense_Mutation

c.887N>C

p.Lys296Thr

p.K296T

P11021

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.997)

TCGA-A8-A08Z-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

HSPA5

SNV

Missense_Mutation

c.211N>A

p.Glu71Lys

p.E71K

P11021

protein_coding

deleterious_low_confidence(0.03)

benign(0.02)

TCGA-AC-A2B8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

chemo

HSPA5

SNV

Missense_Mutation

novel

c.414N>T

p.Lys138Asn

p.K138N

P11021

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.902)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HSPA5

SNV

Missense_Mutation

rs368840257

c.1595G>A

p.Arg532His

p.R532H

P11021

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.956)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

HSPA5

SNV

Missense_Mutation

c.1540N>C

p.Glu514Gln

p.E514Q

P11021

protein_coding

tolerated_low_confidence(0.24)

probably_damaging(0.982)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

HSPA5

SNV

Missense_Mutation

rs191087735

c.395N>C

p.Ile132Thr

p.I132T

P11021

protein_coding

tolerated_low_confidence(0.13)

benign(0.012)

TCGA-E2-A56Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

HSPA5

SNV

Missense_Mutation

novel

c.433N>G

p.Ile145Val

p.I145V

P11021

protein_coding

tolerated_low_confidence(0.38)

benign(0.011)

TCGA-S3-AA12-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

HSPA5

SNV

Missense_Mutation

rs762582529

c.971N>A

p.Arg324Gln

p.R324Q

P11021

protein_coding

deleterious_low_confidence(0.03)

benign(0.368)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

HSPA5

SNV

Missense_Mutation

c.1712N>A

p.Ser571Tyr

p.S571Y

P11021

protein_coding

tolerated_low_confidence(0.05)

benign(0.114)

TCGA-CA-6718-01

Colorectum

colon adenocarcinoma

Male

<65

I/II

Unknown

HSPA5

SNV

Missense_Mutation

novel

c.949N>T

p.Asp317Tyr

p.D317Y

P11021

protein_coding

deleterious_low_confidence(0)

probably_damaging(1)

TCGA-AG-3892-01

Colorectum

rectum adenocarcinoma

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
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		STROBOPININ	STROBOPININ
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		TCMDC-123749	CHEMBL524376
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		NORGESTREL	NORGESTREL
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		MIANSERIN	MIANSERIN
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		AG-490	CHEMBL56543
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		CHLORQUINALDOL	CHLORQUINALDOL
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		SAM-6
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		5-NITRO-2-PHENYLPROPYLAMINOBENZOIC ACID [NPPB]	5-NITRO-2-PHENYLPROPYLAMINOBENZOIC ACID [NPPB]
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		THAPSIGARGIN	THAPSIGARGIN
3309	HSPA5	TRANSPORTER, ENZYME, PROTEASE INHIBITOR, CELL SURFACE, DRUGGABLE GENOME		NKP-1339	IT-139

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