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: SUPT6H

Gene summary for SUPT6H

Gene summary.

Gene information	Species	Human
	Gene symbol	SUPT6H
	Gene ID	6830
	Gene name	SPT6 homolog, histone chaperone and transcription elongation factor
	Gene Alias	SPT6
	Cytomap	17q11.2
	Gene Type	protein-coding
	GO ID	GO:0000018
	UniProtAcc	Q7KZ85

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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
6830	SUPT6H	PTC07	Human	Thyroid	PTC	2.73e-31	4.95e-01	0.2044
6830	SUPT6H	ATC11	Human	Thyroid	ATC	1.91e-04	3.89e-01	0.3386
6830	SUPT6H	ATC12	Human	Thyroid	ATC	5.75e-13	2.60e-01	0.34
6830	SUPT6H	ATC13	Human	Thyroid	ATC	1.77e-23	3.79e-01	0.34
6830	SUPT6H	ATC2	Human	Thyroid	ATC	6.73e-09	8.93e-01	0.34
6830	SUPT6H	ATC3	Human	Thyroid	ATC	3.53e-05	2.39e-01	0.338
6830	SUPT6H	ATC4	Human	Thyroid	ATC	1.14e-14	3.55e-01	0.34
6830	SUPT6H	ATC5	Human	Thyroid	ATC	1.06e-28	4.32e-01	0.34

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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
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:0008380111	Esophagus	ESCC	RNA splicing	336/8552	434/18723	1.74e-42	3.67e-39	336
GO:0006913110	Esophagus	ESCC	nucleocytoplasmic transport	230/8552	301/18723	6.04e-28	2.02e-25	230
GO:0051169110	Esophagus	ESCC	nuclear transport	230/8552	301/18723	6.04e-28	2.02e-25	230
GO:0006403110	Esophagus	ESCC	RNA localization	166/8552	201/18723	1.95e-27	6.18e-25	166
GO:001657015	Esophagus	ESCC	histone modification	323/8552	463/18723	2.61e-26	7.88e-24	323
GO:003238618	Esophagus	ESCC	regulation of intracellular transport	243/8552	337/18723	3.20e-23	7.25e-21	243
GO:1903311110	Esophagus	ESCC	regulation of mRNA metabolic process	210/8552	288/18723	3.25e-21	5.56e-19	210
GO:005123617	Esophagus	ESCC	establishment of RNA localization	134/8552	166/18723	1.23e-20	1.81e-18	134
GO:0051168110	Esophagus	ESCC	nuclear export	126/8552	154/18723	1.88e-20	2.65e-18	126
GO:005102815	Esophagus	ESCC	mRNA transport	110/8552	130/18723	2.76e-20	3.80e-18	110
GO:001820514	Esophagus	ESCC	peptidyl-lysine modification	259/8552	376/18723	3.90e-20	5.26e-18	259
GO:005065717	Esophagus	ESCC	nucleic acid transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:005065817	Esophagus	ESCC	RNA transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:001593117	Esophagus	ESCC	nucleobase-containing compound transport	162/8552	222/18723	9.87e-17	7.93e-15	162
GO:0050684110	Esophagus	ESCC	regulation of mRNA processing	109/8552	137/18723	3.51e-16	2.59e-14	109
GO:000170119	Esophagus	ESCC	in utero embryonic development	243/8552	367/18723	1.00e-15	6.86e-14	243
GO:0046822110	Esophagus	ESCC	regulation of nucleocytoplasmic transport	88/8552	106/18723	1.88e-15	1.19e-13	88
GO:000635414	Esophagus	ESCC	DNA-templated transcription, elongation	76/8552	91/18723	8.35e-14	4.11e-12	76
GO:005105215	Esophagus	ESCC	regulation of DNA metabolic process	232/8552	359/18723	2.40e-13	1.13e-11	232
GO:007116612	Esophagus	ESCC	ribonucleoprotein complex localization	66/8552	77/18723	2.94e-13	1.38e-11	66

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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

SUPT6H

SNV

Missense_Mutation

c.388N>T

p.Asp130Tyr

p.D130Y

Q7KZ85

protein_coding

deleterious(0)

possibly_damaging(0.791)

TCGA-A2-A25A-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unspecific

Cytoxan

SUPT6H

SNV

Missense_Mutation

c.5009N>G

p.Ala1670Gly

p.A1670G

Q7KZ85

protein_coding

tolerated(0.37)

benign(0.066)

TCGA-A7-A0DA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

SUPT6H

SNV

Missense_Mutation

rs755836482

c.4562N>C

p.Gly1521Ala

p.G1521A

Q7KZ85

protein_coding

tolerated(0.12)

possibly_damaging(0.505)

TCGA-A8-A08B-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SUPT6H

SNV

Missense_Mutation

c.3218N>T

p.Ala1073Val

p.A1073V

Q7KZ85

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SUPT6H

SNV

Missense_Mutation

c.3817N>C

p.Glu1273Gln

p.E1273Q

Q7KZ85

protein_coding

deleterious(0.01)

probably_damaging(0.989)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SUPT6H

SNV

Missense_Mutation

c.295G>A

p.Asp99Asn

p.D99N

Q7KZ85

protein_coding

deleterious(0.01)

probably_damaging(0.956)

TCGA-AO-A03T-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

SUPT6H

SNV

Missense_Mutation

c.298N>A

p.Asp100Asn

p.D100N

Q7KZ85

protein_coding

deleterious(0.02)

probably_damaging(0.956)

TCGA-C8-A131-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

SUPT6H

SNV

Missense_Mutation

c.3779G>C

p.Gly1260Ala

p.G1260A

Q7KZ85

protein_coding

deleterious(0.02)

possibly_damaging(0.705)

TCGA-C8-A27B-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

SUPT6H

SNV

Missense_Mutation

c.22N>A

p.Glu8Lys

p.E8K

Q7KZ85

protein_coding

deleterious_low_confidence(0.03)

possibly_damaging(0.905)

TCGA-D8-A1J9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

SUPT6H

SNV

Missense_Mutation

c.388G>T

p.Asp130Tyr

p.D130Y

Q7KZ85

protein_coding

deleterious(0)

possibly_damaging(0.791)

TCGA-D8-A1X7-01

Breast

breast invasive carcinoma

Female

<65

I/II

ChemotherapyHormone Therapy

doxorubicine+cyclophosphamide+tamoxifen

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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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