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: ITGB1BP1

Gene summary for ITGB1BP1

Gene summary.

Gene information	Species	Human
	Gene symbol	ITGB1BP1
	Gene ID	9270
	Gene name	integrin subunit beta 1 binding protein 1
	Gene Alias	ICAP-1A
	Cytomap	2p25.1
	Gene Type	protein-coding
	GO ID	GO:0000165
	UniProtAcc	O14713

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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
9270	ITGB1BP1	LZE4T	Human	Esophagus	ESCC	3.19e-22	7.32e-01	0.0811
9270	ITGB1BP1	LZE5T	Human	Esophagus	ESCC	9.94e-04	2.39e-01	0.0514
9270	ITGB1BP1	LZE7T	Human	Esophagus	ESCC	1.76e-07	6.14e-01	0.0667
9270	ITGB1BP1	LZE20T	Human	Esophagus	ESCC	1.83e-03	2.09e-01	0.0662
9270	ITGB1BP1	LZE22T	Human	Esophagus	ESCC	4.25e-04	9.11e-01	0.068
9270	ITGB1BP1	LZE24T	Human	Esophagus	ESCC	3.49e-19	7.05e-01	0.0596
9270	ITGB1BP1	LZE21T	Human	Esophagus	ESCC	2.61e-04	4.43e-01	0.0655
9270	ITGB1BP1	LZE6T	Human	Esophagus	ESCC	5.81e-10	6.17e-01	0.0845
9270	ITGB1BP1	P1T-E	Human	Esophagus	ESCC	1.52e-09	5.19e-01	0.0875
9270	ITGB1BP1	P2T-E	Human	Esophagus	ESCC	1.05e-32	7.46e-01	0.1177
9270	ITGB1BP1	P4T-E	Human	Esophagus	ESCC	5.40e-38	9.82e-01	0.1323
9270	ITGB1BP1	P5T-E	Human	Esophagus	ESCC	3.34e-48	9.79e-01	0.1327
9270	ITGB1BP1	P8T-E	Human	Esophagus	ESCC	7.49e-31	5.27e-01	0.0889
9270	ITGB1BP1	P9T-E	Human	Esophagus	ESCC	3.25e-28	6.81e-01	0.1131
9270	ITGB1BP1	P10T-E	Human	Esophagus	ESCC	1.51e-57	1.10e+00	0.116
9270	ITGB1BP1	P11T-E	Human	Esophagus	ESCC	6.14e-24	1.15e+00	0.1426
9270	ITGB1BP1	P12T-E	Human	Esophagus	ESCC	4.50e-40	7.29e-01	0.1122
9270	ITGB1BP1	P15T-E	Human	Esophagus	ESCC	7.10e-35	9.40e-01	0.1149
9270	ITGB1BP1	P16T-E	Human	Esophagus	ESCC	9.15e-20	3.67e-01	0.1153
9270	ITGB1BP1	P17T-E	Human	Esophagus	ESCC	1.15e-11	9.66e-01	0.1278

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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
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:003238618	Esophagus	ESCC	regulation of intracellular transport	243/8552	337/18723	3.20e-23	7.25e-21	243
GO:0006605111	Esophagus	ESCC	protein targeting	229/8552	314/18723	4.93e-23	1.01e-20	229
GO:0051098111	Esophagus	ESCC	regulation of binding	251/8552	363/18723	6.73e-20	8.46e-18	251
GO:1903829111	Esophagus	ESCC	positive regulation of cellular protein localization	199/8552	276/18723	2.99e-19	3.45e-17	199
GO:0033157110	Esophagus	ESCC	regulation of intracellular protein transport	169/8552	229/18723	3.31e-18	3.23e-16	169
GO:0032388110	Esophagus	ESCC	positive regulation of intracellular transport	152/8552	202/18723	7.89e-18	7.36e-16	152
GO:1904951111	Esophagus	ESCC	positive regulation of establishment of protein localization	216/8552	319/18723	1.01e-15	6.86e-14	216
GO:0090150110	Esophagus	ESCC	establishment of protein localization to membrane	182/8552	260/18723	1.27e-15	8.19e-14	182
GO:009031617	Esophagus	ESCC	positive regulation of intracellular protein transport	122/8552	160/18723	2.45e-15	1.49e-13	122
GO:0051222111	Esophagus	ESCC	positive regulation of protein transport	204/8552	303/18723	1.56e-14	8.38e-13	204
GO:0072659110	Esophagus	ESCC	protein localization to plasma membrane	193/8552	284/18723	1.95e-14	1.03e-12	193
GO:199077819	Esophagus	ESCC	protein localization to cell periphery	217/8552	333/18723	4.08e-13	1.88e-11	217
GO:0010563111	Esophagus	ESCC	negative regulation of phosphorus metabolic process	274/8552	442/18723	2.32e-12	9.41e-11	274
GO:0045936111	Esophagus	ESCC	negative regulation of phosphate metabolic process	273/8552	441/18723	3.18e-12	1.25e-10	273
GO:0051348111	Esophagus	ESCC	negative regulation of transferase activity	177/8552	268/18723	1.08e-11	4.00e-10	177
GO:004339320	Esophagus	ESCC	regulation of protein binding	135/8552	196/18723	3.69e-11	1.22e-09	135
GO:1902905111	Esophagus	ESCC	positive regulation of supramolecular fiber organization	142/8552	209/18723	5.51e-11	1.76e-09	142
GO:1902903111	Esophagus	ESCC	regulation of supramolecular fiber organization	237/8552	383/18723	9.06e-11	2.75e-09	237
GO:0042326111	Esophagus	ESCC	negative regulation of phosphorylation	237/8552	385/18723	1.86e-10	5.33e-09	237
GO:0150115110	Esophagus	ESCC	cell-substrate junction organization	77/8552	101/18723	3.46e-10	9.57e-09	77

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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

ITGB1BP1

SNV

Missense_Mutation

c.592N>A

p.Glu198Lys

p.E198K

O14713

protein_coding

tolerated(0.25)

benign(0.185)

TCGA-D8-A1XQ-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

c.83N>G

p.Ser28Cys

p.S28C

O14713

protein_coding

tolerated(0.12)

probably_damaging(0.996)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

rs773209764

c.8G>A

p.Arg3His

p.R3H

O14713

protein_coding

deleterious_low_confidence(0.01)

probably_damaging(0.991)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

c.83N>A

p.Ser28Tyr

p.S28Y

O14713

protein_coding

deleterious(0.03)

probably_damaging(0.995)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

ITGB1BP1

SNV

Missense_Mutation

rs376533619

c.317C>T

p.Pro106Leu

p.P106L

O14713

protein_coding

tolerated(0.31)

benign(0.007)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

novel

c.29N>A

p.Ser10Asn

p.S10N

O14713

protein_coding

tolerated_low_confidence(0.19)

probably_damaging(0.95)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

ITGB1BP1

SNV

Missense_Mutation

novel

c.122G>A

p.Ser41Asn

p.S41N

O14713

protein_coding

deleterious(0.03)

probably_damaging(0.988)

TCGA-B5-A1MX-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Hormone Therapy

megace

ITGB1BP1

SNV

Missense_Mutation

novel

c.526N>G

p.Ser176Gly

p.S176G

O14713

protein_coding

tolerated(0.13)

possibly_damaging(0.59)

TCGA-BK-A6W3-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

novel

c.439G>A

p.Gly147Ser

p.G147S

O14713

protein_coding

tolerated(0.27)

probably_damaging(0.999)

TCGA-EO-A22R-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

ITGB1BP1

SNV

Missense_Mutation

rs771640299

c.568N>A

p.Ala190Thr

p.A190T

O14713

protein_coding

tolerated(0.21)

benign(0.207)

TCGA-EO-A22U-01

Endometrium

uterine corpus endometrioid carcinoma

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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