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: IGF2BP1

Gene summary for IGF2BP1

Gene summary.

Gene information	Species	Human
	Gene symbol	IGF2BP1
	Gene ID	10642
	Gene name	insulin like growth factor 2 mRNA binding protein 1
	Gene Alias	CRD-BP
	Cytomap	17q21.32
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	Q9NZI8

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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
10642	IGF2BP1	HCC1_Meng	Human	Liver	HCC	2.55e-72	2.61e-01	0.0246
10642	IGF2BP1	HCC1	Human	Liver	HCC	5.55e-14	4.13e+00	0.5336
10642	IGF2BP1	HCC2	Human	Liver	HCC	3.81e-13	2.95e+00	0.5341
10642	IGF2BP1	S014	Human	Liver	HCC	6.14e-40	1.22e+00	0.2254
10642	IGF2BP1	S015	Human	Liver	HCC	4.14e-41	1.47e+00	0.2375
10642	IGF2BP1	S016	Human	Liver	HCC	2.63e-50	1.26e+00	0.2243

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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:004427021	Liver	HCC	cellular nitrogen compound catabolic process	303/7958	451/18723	9.76e-27	3.64e-24	303
GO:004670021	Liver	HCC	heterocycle catabolic process	299/7958	445/18723	2.07e-26	7.29e-24	299
GO:190136121	Liver	HCC	organic cyclic compound catabolic process	325/7958	495/18723	6.52e-26	2.18e-23	325
GO:001943921	Liver	HCC	aromatic compound catabolic process	309/7958	467/18723	1.56e-25	4.94e-23	309
GO:000640121	Liver	HCC	RNA catabolic process	201/7958	278/18723	3.88e-24	1.02e-21	201
GO:003465521	Liver	HCC	nucleobase-containing compound catabolic process	273/7958	407/18723	4.84e-24	1.23e-21	273
GO:190331121	Liver	HCC	regulation of mRNA metabolic process	205/7958	288/18723	3.38e-23	6.90e-21	205
GO:000640321	Liver	HCC	RNA localization	151/7958	201/18723	3.72e-21	5.89e-19	151
GO:000640221	Liver	HCC	mRNA catabolic process	169/7958	232/18723	4.50e-21	6.96e-19	169
GO:000641722	Liver	HCC	regulation of translation	287/7958	468/18723	8.79e-17	8.08e-15	287
GO:005123621	Liver	HCC	establishment of RNA localization	121/7958	166/18723	1.61e-15	1.19e-13	121
GO:005065711	Liver	HCC	nucleic acid transport	118/7958	163/18723	8.30e-15	5.60e-13	118
GO:005065811	Liver	HCC	RNA transport	118/7958	163/18723	8.30e-15	5.60e-13	118
GO:001593111	Liver	HCC	nucleobase-containing compound transport	150/7958	222/18723	3.17e-14	2.03e-12	150
GO:005102811	Liver	HCC	mRNA transport	97/7958	130/18723	9.00e-14	5.23e-12	97
GO:004348721	Liver	HCC	regulation of RNA stability	119/7958	170/18723	3.20e-13	1.71e-11	119
GO:004348821	Liver	HCC	regulation of mRNA stability	110/7958	158/18723	4.36e-12	1.93e-10	110
GO:006101321	Liver	HCC	regulation of mRNA catabolic process	114/7958	166/18723	7.38e-12	3.12e-10	114
GO:000989522	Liver	HCC	negative regulation of catabolic process	196/7958	320/18723	7.98e-12	3.35e-10	196
GO:003133022	Liver	HCC	negative regulation of cellular catabolic process	164/7958	262/18723	3.52e-11	1.35e-09	164

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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

IGF2BP1

SNV

Missense_Mutation

c.718N>A

p.Ala240Thr

p.A240T

Q9NZI8

protein_coding

tolerated(0.17)

benign(0.088)

TCGA-B6-A0I2-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

IGF2BP1

SNV

Missense_Mutation

rs557111796

c.500G>A

p.Arg167His

p.R167H

Q9NZI8

protein_coding

deleterious(0.03)

benign(0.007)

TCGA-D8-A73U-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

IGF2BP1

insertion

In_Frame_Ins

novel

c.815_816insTTTGTGTCATAGGCTGTGTTCTTGTCCCCAACCACTGCTTGCTTATTT

p.Lys272delinsAsnLeuCysHisArgLeuCysSerCysProGlnProLeuLeuAlaTyrLeu

p.K272delinsNLCHRLCSCPQPLLAYL

Q9NZI8

protein_coding

TCGA-AN-A049-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

IGF2BP1

insertion

Frame_Shift_Ins

novel

c.1340_1341insACAGCATCCCTTGGCAGCCCAGGGTGGCGGTTTGG

p.Asp448GlnfsTer51

p.D448Qfs*51

Q9NZI8

protein_coding

TCGA-AO-A0J3-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

cyclophosphamide

IGF2BP1

insertion

Nonsense_Mutation

novel

c.1007_1008insCAGTGTGCTTCGTTTCATCAGAGACTAACCTGTGGGCAAAGTAA

p.Cys337SerfsTer9

p.C337Sfs*9

Q9NZI8

protein_coding

TCGA-BH-A0HB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

IGF2BP1

SNV

Missense_Mutation

c.314N>C

p.Gly105Ala

p.G105A

Q9NZI8

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

IGF2BP1

SNV

Missense_Mutation

c.970G>A

p.Glu324Lys

p.E324K

Q9NZI8

protein_coding

deleterious(0.03)

probably_damaging(0.951)

TCGA-JW-A5VL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

IGF2BP1

SNV

Missense_Mutation

c.1320N>C

p.Lys440Asn

p.K440N

Q9NZI8

protein_coding

deleterious(0)

probably_damaging(0.991)

TCGA-Q1-A5R2-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

IGF2BP1

SNV

Missense_Mutation

rs781338712

c.1501C>T

p.Arg501Trp

p.R501W

Q9NZI8

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-Q1-A6DT-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

IGF2BP1

SNV

Missense_Mutation

novel

c.1381N>A

p.Glu461Lys

p.E461K

Q9NZI8

protein_coding

deleterious(0)

probably_damaging(0.988)

TCGA-VS-A9UP-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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