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: SHANK3

Gene summary for SHANK3

Gene summary.

Gene information	Species	Human
	Gene symbol	SHANK3
	Gene ID	85358
	Gene name	SH3 and multiple ankyrin repeat domains 3
	Gene Alias	DEL22q13.3
	Cytomap	22q13.33
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	NA

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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
85358	SHANK3	HCC1_Meng	Human	Liver	HCC	5.86e-26	4.08e-02	0.0246
85358	SHANK3	HCC1	Human	Liver	HCC	9.16e-05	1.69e+00	0.5336
85358	SHANK3	HCC2	Human	Liver	HCC	7.14e-12	1.55e+00	0.5341

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Liver		HCC: Hepatocellular carcinoma
Liver		NAFLD: Non-alcoholic fatty liver disease

∗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:190290322	Liver	HCC	regulation of supramolecular fiber organization	224/7958	383/18723	1.54e-10	5.33e-09	224
GO:000701522	Liver	HCC	actin filament organization	252/7958	442/18723	3.83e-10	1.25e-08	252
GO:001063912	Liver	HCC	negative regulation of organelle organization	204/7958	348/18723	7.67e-10	2.37e-08	204
GO:003253522	Liver	HCC	regulation of cellular component size	217/7958	383/18723	1.28e-08	3.14e-07	217
GO:003297022	Liver	HCC	regulation of actin filament-based process	222/7958	397/18723	3.81e-08	8.30e-07	222
GO:003295622	Liver	HCC	regulation of actin cytoskeleton organization	202/7958	358/18723	6.18e-08	1.29e-06	202
GO:011005322	Liver	HCC	regulation of actin filament organization	158/7958	278/18723	9.01e-07	1.37e-05	158
GO:005101722	Liver	HCC	actin filament bundle assembly	96/7958	157/18723	1.81e-06	2.52e-05	96
GO:006157222	Liver	HCC	actin filament bundle organization	97/7958	161/18723	4.04e-06	5.22e-05	97
GO:001072011	Liver	HCC	positive regulation of cell development	155/7958	298/18723	5.39e-04	3.48e-03	155
GO:001097511	Liver	HCC	regulation of neuron projection development	220/7958	445/18723	1.68e-03	8.78e-03	220
GO:190290412	Liver	HCC	negative regulation of supramolecular fiber organization	90/7958	167/18723	1.90e-03	9.69e-03	90
GO:00096124	Liver	HCC	response to mechanical stimulus	113/7958	216/18723	2.20e-03	1.10e-02	113
GO:00507674	Liver	HCC	regulation of neurogenesis	181/7958	364/18723	3.00e-03	1.40e-02	181
GO:0060999	Liver	HCC	positive regulation of dendritic spine development	27/7958	42/18723	3.60e-03	1.60e-02	27
GO:00507693	Liver	HCC	positive regulation of neurogenesis	116/7958	225/18723	3.67e-03	1.63e-02	116
GO:00083614	Liver	HCC	regulation of cell size	95/7958	181/18723	4.15e-03	1.81e-02	95
GO:003223122	Liver	HCC	regulation of actin filament bundle assembly	57/7958	105/18723	9.73e-03	3.66e-02	57
GO:006099611	Liver	HCC	dendritic spine development	54/7958	99/18723	1.03e-02	3.86e-02	54
GO:00514946	Liver	HCC	negative regulation of cytoskeleton organization	84/7958	163/18723	1.22e-02	4.43e-02	84

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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

SHANK3

SNV

Missense_Mutation

novel

c.1266T>G

p.Ser422Arg

p.S422R

protein_coding

tolerated(0.61)

benign(0.162)

TCGA-A1-A0SP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

SHANK3

SNV

Missense_Mutation

rs758053583

c.899N>A

p.Arg300His

p.R300H

protein_coding

deleterious(0)

possibly_damaging(0.689)

TCGA-A2-A1G0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

SHANK3

SNV

Missense_Mutation

c.1604N>A

p.Arg535Gln

p.R535Q

protein_coding

tolerated(0.26)

benign(0.23)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SHANK3

SNV

Missense_Mutation

c.4091N>G

p.Ser1364Cys

p.S1364C

protein_coding

deleterious(0.01)

possibly_damaging(0.571)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

SHANK3

SNV

Missense_Mutation

c.1783N>A

p.Glu595Lys

p.E595K

protein_coding

deleterious(0)

probably_damaging(0.997)

TCGA-C8-A138-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

SHANK3

deletion

Frame_Shift_Del

novel

c.4014delG

p.Lys1339SerfsTer46

p.K1339Sfs*46

protein_coding

TCGA-EW-A2FV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

docetaxel

SHANK3

SNV

Missense_Mutation

rs770978141

c.4382G>A

p.Arg1461His

p.R1461H

protein_coding

deleterious(0.02)

probably_damaging(0.991)

TCGA-EA-A410-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SHANK3

insertion

Nonsense_Mutation

novel

c.2018_2019insATGAGGAA

p.Arg674Ter

p.R674*

protein_coding

TCGA-DS-A1OB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

carboplatin

SHANK3

deletion

Frame_Shift_Del

novel

c.4184delN

p.His1395ProfsTer32

p.H1395Pfs*32

protein_coding

TCGA-EA-A3HU-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

SHANK3

SNV

Missense_Mutation

novel

c.4967N>A

p.Arg1656His

p.R1656H

protein_coding

tolerated(0.12)

possibly_damaging(0.646)

TCGA-5M-AAT6-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

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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