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: IDH1

Gene summary for IDH1

Gene summary.

Gene information	Species	Human
	Gene symbol	IDH1
	Gene ID	3417
	Gene name	isocitrate dehydrogenase (NADP(+)) 1
	Gene Alias	HEL-216
	Cytomap	2q34
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	O75874

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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
3417	IDH1	HTA11_78_2000001011	Human	Colorectum	AD	7.60e-07	7.30e-01	-0.1088
3417	IDH1	HTA11_347_2000001011	Human	Colorectum	AD	6.76e-17	9.29e-01	-0.1954
3417	IDH1	HTA11_99999970781_79442	Human	Colorectum	MSS	8.70e-21	9.46e-01	0.294
3417	IDH1	HTA11_99999971662_82457	Human	Colorectum	MSS	4.74e-07	4.98e-01	0.3859
3417	IDH1	F007	Human	Colorectum	FAP	1.08e-03	-2.19e-01	0.1176
3417	IDH1	A002-C-010	Human	Colorectum	FAP	4.74e-02	-1.78e-01	0.242
3417	IDH1	A001-C-207	Human	Colorectum	FAP	3.09e-03	-2.09e-01	0.1278
3417	IDH1	A015-C-203	Human	Colorectum	FAP	8.12e-13	-2.70e-01	-0.1294
3417	IDH1	A015-C-204	Human	Colorectum	FAP	3.87e-03	-1.68e-01	-0.0228
3417	IDH1	A014-C-040	Human	Colorectum	FAP	5.09e-04	-3.40e-01	-0.1184
3417	IDH1	A002-C-201	Human	Colorectum	FAP	1.23e-11	-2.70e-01	0.0324
3417	IDH1	A002-C-203	Human	Colorectum	FAP	7.80e-06	-1.71e-01	0.2786
3417	IDH1	A001-C-119	Human	Colorectum	FAP	1.33e-06	-2.79e-01	-0.1557
3417	IDH1	A001-C-108	Human	Colorectum	FAP	6.19e-11	-2.66e-01	-0.0272
3417	IDH1	A002-C-205	Human	Colorectum	FAP	5.81e-15	-3.12e-01	-0.1236
3417	IDH1	A001-C-104	Human	Colorectum	FAP	1.84e-03	-2.34e-01	0.0184
3417	IDH1	A015-C-005	Human	Colorectum	FAP	8.72e-07	-2.46e-01	-0.0336
3417	IDH1	A015-C-006	Human	Colorectum	FAP	1.54e-08	-2.51e-01	-0.0994
3417	IDH1	A015-C-106	Human	Colorectum	FAP	3.39e-08	-2.78e-01	-0.0511
3417	IDH1	A002-C-114	Human	Colorectum	FAP	4.44e-09	-2.46e-01	-0.1561

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
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:0006091	Colorectum	AD	generation of precursor metabolites and energy	209/3918	490/18723	3.17e-28	6.61e-25	209
GO:0009060	Colorectum	AD	aerobic respiration	108/3918	189/18723	9.14e-28	1.43e-24	108
GO:0045333	Colorectum	AD	cellular respiration	119/3918	230/18723	3.21e-25	4.02e-22	119
GO:0015980	Colorectum	AD	energy derivation by oxidation of organic compounds	143/3918	318/18723	2.78e-22	2.49e-19	143
GO:0006979	Colorectum	AD	response to oxidative stress	145/3918	446/18723	5.16e-09	3.23e-07	145
GO:0006099	Colorectum	AD	tricarboxylic acid cycle	19/3918	30/18723	5.82e-07	2.09e-05	19
GO:0048545	Colorectum	AD	response to steroid hormone	104/3918	339/18723	1.33e-05	2.90e-04	104
GO:0006066	Colorectum	AD	alcohol metabolic process	106/3918	353/18723	3.02e-05	5.57e-04	106
GO:0016042	Colorectum	AD	lipid catabolic process	97/3918	320/18723	4.31e-05	7.56e-04	97
GO:0044262	Colorectum	AD	cellular carbohydrate metabolic process	87/3918	283/18723	6.00e-05	1.01e-03	87
GO:0006790	Colorectum	AD	sulfur compound metabolic process	101/3918	339/18723	6.46e-05	1.07e-03	101
GO:0044242	Colorectum	AD	cellular lipid catabolic process	66/3918	214/18723	3.96e-04	4.50e-03	66
GO:0006575	Colorectum	AD	cellular modified amino acid metabolic process	59/3918	188/18723	4.80e-04	5.27e-03	59
GO:0043648	Colorectum	AD	dicarboxylic acid metabolic process	34/3918	96/18723	7.22e-04	7.28e-03	34
GO:0061458	Colorectum	AD	reproductive system development	116/3918	427/18723	1.11e-03	1.01e-02	116
GO:0048608	Colorectum	AD	reproductive structure development	114/3918	424/18723	1.78e-03	1.47e-02	114
GO:0006081	Colorectum	AD	cellular aldehyde metabolic process	22/3918	60/18723	3.64e-03	2.60e-02	22
GO:0006644	Colorectum	AD	phospholipid metabolic process	101/3918	383/18723	5.80e-03	3.67e-02	101
GO:00090602	Colorectum	MSS	aerobic respiration	98/3467	189/18723	3.35e-25	1.05e-21	98
GO:00060912	Colorectum	MSS	generation of precursor metabolites and energy	186/3467	490/18723	1.14e-24	2.15e-21	186

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa01200	Colorectum	AD	Carbon metabolism	55/2092	115/8465	5.53e-08	8.42e-07	5.37e-07	55
hsa00020	Colorectum	AD	Citrate cycle (TCA cycle)	20/2092	30/8465	1.43e-06	1.77e-05	1.13e-05	20
hsa05230	Colorectum	AD	Central carbon metabolism in cancer	33/2092	70/8465	3.61e-05	3.19e-04	2.03e-04	33
hsa00480	Colorectum	AD	Glutathione metabolism	23/2092	57/8465	6.52e-03	2.76e-02	1.76e-02	23
hsa01230	Colorectum	AD	Biosynthesis of amino acids	28/2092	75/8465	9.99e-03	3.89e-02	2.48e-02	28
hsa012001	Colorectum	AD	Carbon metabolism	55/2092	115/8465	5.53e-08	8.42e-07	5.37e-07	55
hsa000201	Colorectum	AD	Citrate cycle (TCA cycle)	20/2092	30/8465	1.43e-06	1.77e-05	1.13e-05	20
hsa052301	Colorectum	AD	Central carbon metabolism in cancer	33/2092	70/8465	3.61e-05	3.19e-04	2.03e-04	33
hsa004801	Colorectum	AD	Glutathione metabolism	23/2092	57/8465	6.52e-03	2.76e-02	1.76e-02	23
hsa012301	Colorectum	AD	Biosynthesis of amino acids	28/2092	75/8465	9.99e-03	3.89e-02	2.48e-02	28
hsa012004	Colorectum	MSS	Carbon metabolism	43/1875	115/8465	1.37e-04	1.17e-03	7.19e-04	43
hsa000204	Colorectum	MSS	Citrate cycle (TCA cycle)	16/1875	30/8465	1.84e-04	1.47e-03	9.00e-04	16
hsa004802	Colorectum	MSS	Glutathione metabolism	22/1875	57/8465	3.58e-03	1.64e-02	1.01e-02	22
hsa052304	Colorectum	MSS	Central carbon metabolism in cancer	25/1875	70/8465	6.50e-03	2.64e-02	1.62e-02	25
hsa012005	Colorectum	MSS	Carbon metabolism	43/1875	115/8465	1.37e-04	1.17e-03	7.19e-04	43
hsa000205	Colorectum	MSS	Citrate cycle (TCA cycle)	16/1875	30/8465	1.84e-04	1.47e-03	9.00e-04	16
hsa004803	Colorectum	MSS	Glutathione metabolism	22/1875	57/8465	3.58e-03	1.64e-02	1.01e-02	22
hsa052305	Colorectum	MSS	Central carbon metabolism in cancer	25/1875	70/8465	6.50e-03	2.64e-02	1.62e-02	25
hsa012006	Colorectum	FAP	Carbon metabolism	38/1404	115/8465	1.04e-05	1.44e-04	8.76e-05	38
hsa052306	Colorectum	FAP	Central carbon metabolism in cancer	23/1404	70/8465	6.12e-04	4.26e-03	2.59e-03	23

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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

IDH1

SNV

Missense_Mutation

novel

c.453N>T

p.Lys151Asn

p.K151N

O75874

protein_coding

deleterious_low_confidence(0)

possibly_damaging(0.48)

TCGA-A2-A0T0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

IDH1

SNV

Missense_Mutation

c.1013N>C

p.Arg338Thr

p.R338T

O75874

protein_coding

deleterious_low_confidence(0.01)

possibly_damaging(0.74)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

IDH1

SNV

Missense_Mutation

c.243N>C

p.Lys81Asn

p.K81N

O75874

protein_coding

tolerated_low_confidence(0.13)

benign(0.014)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

IDH1

SNV

Missense_Mutation

c.704N>G

p.Tyr235Cys

p.Y235C

O75874

protein_coding

deleterious_low_confidence(0)

probably_damaging(1)

TCGA-BH-A0DD-01

Breast

breast invasive carcinoma

Male

<65

I/II

Chemotherapy

docetaxel

IDH1

SNV

Missense_Mutation

rs121913499

c.394N>T

p.Arg132Cys

p.R132C

O75874

protein_coding

deleterious_low_confidence(0.03)

benign(0.1)

TCGA-BH-A1FR-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

IDH1

SNV

Missense_Mutation

rs121913500

c.395N>A

p.Arg132His

p.R132H

O75874

protein_coding

deleterious_low_confidence(0.01)

benign(0.047)

TCGA-S3-AA11-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

letrozole

IDH1

SNV

Missense_Mutation

novel

c.544A>T

p.Met182Leu

p.M182L

O75874

protein_coding

deleterious_low_confidence(0)

benign(0.228)

TCGA-AA-3947-01

Colorectum

colon adenocarcinoma

Female

<65

I/II

Unknown

IDH1

SNV

Missense_Mutation

rs555882127

c.97C>T

p.Pro33Ser

p.P33S

O75874

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.998)

TCGA-AA-3949-01

Colorectum

colon adenocarcinoma

Female

>=65

III/IV

Unknown

IDH1

SNV

Missense_Mutation

rs781398075

c.103G>A

p.Val35Met

p.V35M

O75874

protein_coding

deleterious_low_confidence(0.01)

benign(0.129)

TCGA-AD-5900-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

IDH1

SNV

Missense_Mutation

c.377N>G

p.Lys126Arg

p.K126R

O75874

protein_coding

deleterious_low_confidence(0.03)

possibly_damaging(0.683)

TCGA-AZ-6598-01

Colorectum

colon 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
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		BPTES		21045145
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		GNF-PF-67	CHEMBL578512
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		BAY1436032		28232670
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		CP-55940	CP-55940
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		BI-87E7	CHEMBL523200
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		1-BENZYLMALEIMIDE	CHEMBL388979
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		VENETOCLAX	VENETOCLAX	30725494
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		CANDIDIN	CANDIDIN
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		SANGUINARIUM CHLORIDE	SANGUINARIUM CHLORIDE
3417	IDH1	ENZYME, CLINICALLY ACTIONABLE		DNDI1318477	CHEMBL428064

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