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: BAIAP2L1

Gene summary for BAIAP2L1

Gene summary.

Gene information	Species	Human
	Gene symbol	BAIAP2L1
	Gene ID	55971
	Gene name	BAR/IMD domain containing adaptor protein 2 like 1
	Gene Alias	IRTKS
	Cytomap	7q21.3-q22.1
	Gene Type	protein-coding
	GO ID	GO:0006996
	UniProtAcc	Q9UHR4

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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
55971	BAIAP2L1	CCI_1	Human	Cervix	CC	4.98e-32	2.11e+00	0.528
55971	BAIAP2L1	CCI_2	Human	Cervix	CC	6.19e-26	1.76e+00	0.5249
55971	BAIAP2L1	CCI_3	Human	Cervix	CC	1.38e-33	1.35e+00	0.516
55971	BAIAP2L1	CCII_1	Human	Cervix	CC	4.47e-15	5.54e-01	0.3249
55971	BAIAP2L1	sample3	Human	Cervix	CC	1.15e-12	3.07e-01	0.1387
55971	BAIAP2L1	H2	Human	Cervix	HSIL_HPV	6.78e-03	1.89e-01	0.0632
55971	BAIAP2L1	T1	Human	Cervix	CC	9.20e-03	2.37e-01	0.0918
55971	BAIAP2L1	T3	Human	Cervix	CC	2.89e-11	2.77e-01	0.1389
55971	BAIAP2L1	HTA11_3410_2000001011	Human	Colorectum	AD	6.66e-05	-3.53e-01	0.0155
55971	BAIAP2L1	HTA11_1938_2000001011	Human	Colorectum	AD	1.30e-05	6.33e-01	-0.0811
55971	BAIAP2L1	HTA11_347_2000001011	Human	Colorectum	AD	7.93e-04	4.60e-01	-0.1954
55971	BAIAP2L1	HTA11_411_2000001011	Human	Colorectum	SER	3.11e-05	1.33e+00	-0.2602
55971	BAIAP2L1	HTA11_2112_2000001011	Human	Colorectum	SER	2.30e-03	9.37e-01	-0.2196
55971	BAIAP2L1	HTA11_99999965104_69814	Human	Colorectum	MSS	7.33e-08	8.04e-01	0.281
55971	BAIAP2L1	HTA11_99999971662_82457	Human	Colorectum	MSS	8.42e-03	4.46e-01	0.3859
55971	BAIAP2L1	F007	Human	Colorectum	FAP	2.12e-04	-3.53e-01	0.1176
55971	BAIAP2L1	A001-C-207	Human	Colorectum	FAP	2.57e-02	-1.60e-01	0.1278
55971	BAIAP2L1	A015-C-203	Human	Colorectum	FAP	1.07e-28	-4.14e-01	-0.1294
55971	BAIAP2L1	A015-C-204	Human	Colorectum	FAP	7.38e-07	-2.99e-01	-0.0228
55971	BAIAP2L1	A014-C-040	Human	Colorectum	FAP	4.58e-07	-5.37e-01	-0.1184

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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

∗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:19016531	Colorectum	SER	cellular response to peptide	83/2897	359/18723	8.03e-05	1.77e-03	83
GO:00434341	Colorectum	SER	response to peptide hormone	93/2897	414/18723	9.61e-05	2.04e-03	93
GO:00713751	Colorectum	SER	cellular response to peptide hormone stimulus	68/2897	290/18723	2.20e-04	3.89e-03	68
GO:00328691	Colorectum	SER	cellular response to insulin stimulus	51/2897	203/18723	2.30e-04	3.96e-03	51
GO:00315321	Colorectum	SER	actin cytoskeleton reorganization	30/2897	107/18723	6.38e-04	8.64e-03	30
GO:0007009	Colorectum	SER	plasma membrane organization	36/2897	142/18723	1.50e-03	1.62e-02	36
GO:00070152	Colorectum	MSS	actin filament organization	146/3467	442/18723	1.16e-13	2.67e-11	146
GO:00325352	Colorectum	MSS	regulation of cellular component size	127/3467	383/18723	3.44e-12	5.79e-10	127
GO:00329702	Colorectum	MSS	regulation of actin filament-based process	128/3467	397/18723	2.47e-11	3.49e-09	128
GO:19029032	Colorectum	MSS	regulation of supramolecular fiber organization	121/3467	383/18723	3.63e-10	3.28e-08	121
GO:00322712	Colorectum	MSS	regulation of protein polymerization	83/3467	233/18723	3.99e-10	3.49e-08	83
GO:00081542	Colorectum	MSS	actin polymerization or depolymerization	79/3467	218/18723	4.14e-10	3.49e-08	79
GO:00300412	Colorectum	MSS	actin filament polymerization	71/3467	191/18723	8.77e-10	6.92e-08	71
GO:00080642	Colorectum	MSS	regulation of actin polymerization or depolymerization	70/3467	188/18723	1.06e-09	8.25e-08	70
GO:00308322	Colorectum	MSS	regulation of actin filament length	70/3467	189/18723	1.38e-09	1.03e-07	70
GO:00432542	Colorectum	MSS	regulation of protein-containing complex assembly	130/3467	428/18723	1.38e-09	1.03e-07	130
GO:00329562	Colorectum	MSS	regulation of actin cytoskeleton organization	113/3467	358/18723	1.46e-09	1.07e-07	113
GO:19029052	Colorectum	MSS	positive regulation of supramolecular fiber organization	75/3467	209/18723	1.89e-09	1.35e-07	75
GO:00308332	Colorectum	MSS	regulation of actin filament polymerization	65/3467	172/18723	2.05e-09	1.45e-07	65
GO:00313342	Colorectum	MSS	positive regulation of protein-containing complex assembly	82/3467	237/18723	2.49e-09	1.75e-07	82

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0513020	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa05130110	Cervix	CC	Pathogenic Escherichia coli infection	63/1267	197/8465	9.28e-10	2.00e-08	1.19e-08	63
hsa0513025	Cervix	HSIL_HPV	Pathogenic Escherichia coli infection	28/459	197/8465	2.36e-06	4.61e-05	3.73e-05	28
hsa0513035	Cervix	HSIL_HPV	Pathogenic Escherichia coli infection	28/459	197/8465	2.36e-06	4.61e-05	3.73e-05	28
hsa05130	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa051301	Colorectum	AD	Pathogenic Escherichia coli infection	79/2092	197/8465	1.05e-06	1.36e-05	8.65e-06	79
hsa051302	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa051303	Colorectum	SER	Pathogenic Escherichia coli infection	60/1580	197/8465	3.63e-05	4.31e-04	3.13e-04	60
hsa051304	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa051305	Colorectum	MSS	Pathogenic Escherichia coli infection	73/1875	197/8465	1.10e-06	1.48e-05	9.06e-06	73
hsa051308	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa051309	Colorectum	FAP	Pathogenic Escherichia coli infection	62/1404	197/8465	1.37e-07	3.08e-06	1.87e-06	62
hsa0513010	Colorectum	CRC	Pathogenic Escherichia coli infection	47/1091	197/8465	1.49e-05	3.84e-04	2.60e-04	47
hsa0513011	Colorectum	CRC	Pathogenic Escherichia coli infection	47/1091	197/8465	1.49e-05	3.84e-04	2.60e-04	47
hsa0513026	Endometrium	AEH	Pathogenic Escherichia coli infection	50/1197	197/8465	1.72e-05	1.86e-04	1.36e-04	50
hsa05130112	Endometrium	AEH	Pathogenic Escherichia coli infection	50/1197	197/8465	1.72e-05	1.86e-04	1.36e-04	50
hsa0513027	Endometrium	EEC	Pathogenic Escherichia coli infection	51/1237	197/8465	1.98e-05	2.28e-04	1.70e-04	51
hsa0513036	Endometrium	EEC	Pathogenic Escherichia coli infection	51/1237	197/8465	1.98e-05	2.28e-04	1.70e-04	51
hsa0513039	Esophagus	HGIN	Pathogenic Escherichia coli infection	54/1383	197/8465	4.91e-05	6.15e-04	4.89e-04	54
hsa05130115	Esophagus	HGIN	Pathogenic Escherichia coli infection	54/1383	197/8465	4.91e-05	6.15e-04	4.89e-04	54

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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

BAIAP2L1

SNV

Missense_Mutation

novel

c.1051N>G

p.Thr351Ala

p.T351A

Q9UHR4

protein_coding

tolerated(0.78)

possibly_damaging(0.469)

TCGA-A7-A6VY-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

BAIAP2L1

SNV

Missense_Mutation

rs775381596

c.601T>C

p.Cys201Arg

p.C201R

Q9UHR4

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

BAIAP2L1

SNV

Missense_Mutation

c.506N>G

p.Ser169Cys

p.S169C

Q9UHR4

protein_coding

deleterious(0.02)

benign(0.28)

TCGA-AR-A0TS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

BAIAP2L1

SNV

Missense_Mutation

rs140166928

c.452N>A

p.Arg151Gln

p.R151Q

Q9UHR4

protein_coding

deleterious(0.03)

benign(0.046)

TCGA-D8-A1J9-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

BAIAP2L1

insertion

Nonsense_Mutation

novel

c.510_511insGCAACACATGTCACATTTCCTTTCCTTTGTTTTAAATTATGA

p.Arg170_Gln171insAlaThrHisValThrPheProPheLeuCysPheLysLeuTer

p.R170_Q171insATHVTFPFLCFKL*

Q9UHR4

protein_coding

TCGA-A8-A092-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

BAIAP2L1

deletion

Frame_Shift_Del

novel

c.1148delN

p.His383ProfsTer26

p.H383Pfs*26

Q9UHR4

protein_coding

TCGA-EW-A2FV-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

docetaxel

BAIAP2L1

SNV

Missense_Mutation

novel

c.986N>T

p.Ser329Leu

p.S329L

Q9UHR4

protein_coding

deleterious(0.02)

probably_damaging(0.995)

TCGA-C5-A2M1-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

BAIAP2L1

SNV

Missense_Mutation

novel

c.1041N>G

p.Ile347Met

p.I347M

Q9UHR4

protein_coding

deleterious(0)

probably_damaging(0.976)

TCGA-DG-A2KM-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

BAIAP2L1

SNV

Missense_Mutation

rs202012767

c.127N>A

p.Ala43Thr

p.A43T

Q9UHR4

protein_coding

deleterious(0.04)

benign(0.116)

TCGA-PN-A8MA-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

BAIAP2L1

SNV

Missense_Mutation

c.842N>T

p.Ser281Leu

p.S281L

Q9UHR4

protein_coding

tolerated(0.28)

benign(0.001)

TCGA-UC-A7PF-01

Cervix

cervical & endocervical cancer

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

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