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: CKAP2

Gene summary for CKAP2

Gene summary.

Gene information	Species	Human
	Gene symbol	CKAP2
	Gene ID	26586
	Gene name	cytoskeleton associated protein 2
	Gene Alias	LB1
	Cytomap	13q14.3
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	Q8WWK9

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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
26586	CKAP2	LZE4T	Human	Esophagus	ESCC	1.86e-06	3.10e-01	0.0811
26586	CKAP2	LZE7T	Human	Esophagus	ESCC	1.52e-06	2.49e-01	0.0667
26586	CKAP2	LZE24T	Human	Esophagus	ESCC	1.40e-11	3.01e-01	0.0596
26586	CKAP2	LZE21T	Human	Esophagus	ESCC	1.31e-02	2.42e-01	0.0655
26586	CKAP2	LZE6T	Human	Esophagus	ESCC	4.54e-04	1.85e-01	0.0845
26586	CKAP2	P1T-E	Human	Esophagus	ESCC	1.09e-05	4.76e-01	0.0875
26586	CKAP2	P2T-E	Human	Esophagus	ESCC	2.93e-25	7.54e-01	0.1177
26586	CKAP2	P4T-E	Human	Esophagus	ESCC	3.38e-26	8.19e-01	0.1323
26586	CKAP2	P5T-E	Human	Esophagus	ESCC	1.81e-10	3.98e-01	0.1327
26586	CKAP2	P8T-E	Human	Esophagus	ESCC	1.49e-03	2.28e-01	0.0889
26586	CKAP2	P9T-E	Human	Esophagus	ESCC	4.76e-08	3.67e-01	0.1131
26586	CKAP2	P10T-E	Human	Esophagus	ESCC	9.01e-20	6.46e-01	0.116
26586	CKAP2	P11T-E	Human	Esophagus	ESCC	1.66e-03	1.88e-01	0.1426
26586	CKAP2	P12T-E	Human	Esophagus	ESCC	3.34e-17	4.43e-01	0.1122
26586	CKAP2	P15T-E	Human	Esophagus	ESCC	1.51e-10	3.41e-01	0.1149
26586	CKAP2	P16T-E	Human	Esophagus	ESCC	3.41e-13	3.70e-01	0.1153
26586	CKAP2	P17T-E	Human	Esophagus	ESCC	6.41e-09	6.91e-01	0.1278
26586	CKAP2	P19T-E	Human	Esophagus	ESCC	1.01e-04	5.37e-01	0.1662
26586	CKAP2	P20T-E	Human	Esophagus	ESCC	5.41e-30	8.10e-01	0.1124
26586	CKAP2	P21T-E	Human	Esophagus	ESCC	3.08e-17	5.84e-01	0.1617

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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:0010639111	Skin	cSCC	negative regulation of organelle organization	140/4864	348/18723	3.35e-09	1.15e-07	140
GO:003298418	Skin	cSCC	protein-containing complex disassembly	98/4864	224/18723	5.31e-09	1.77e-07	98
GO:190290329	Skin	cSCC	regulation of supramolecular fiber organization	145/4864	383/18723	1.67e-07	3.71e-06	145
GO:007050716	Skin	cSCC	regulation of microtubule cytoskeleton organization	61/4864	148/18723	3.61e-05	3.90e-04	61
GO:003288612	Skin	cSCC	regulation of microtubule-based process	82/4864	240/18723	2.82e-03	1.58e-02	82
GO:190290425	Skin	cSCC	negative regulation of supramolecular fiber organization	59/4864	167/18723	4.56e-03	2.33e-02	59
GO:003110911	Skin	cSCC	microtubule polymerization or depolymerization	45/4864	122/18723	5.05e-03	2.56e-02	45
GO:004362411	Skin	cSCC	cellular protein complex disassembly	49/4864	136/18723	6.00e-03	2.95e-02	49
GO:0022411113	Thyroid	PTC	cellular component disassembly	232/5968	443/18723	1.36e-19	1.75e-17	232
GO:1902903113	Thyroid	PTC	regulation of supramolecular fiber organization	202/5968	383/18723	1.16e-17	1.15e-15	202
GO:0032984110	Thyroid	PTC	protein-containing complex disassembly	114/5968	224/18723	2.26e-09	6.33e-08	114
GO:0010639112	Thyroid	PTC	negative regulation of organelle organization	163/5968	348/18723	3.04e-09	8.39e-08	163
GO:007050717	Thyroid	PTC	regulation of microtubule cytoskeleton organization	80/5968	148/18723	1.79e-08	4.19e-07	80
GO:00002818	Thyroid	PTC	mitotic cytokinesis	43/5968	71/18723	5.93e-07	9.47e-06	43
GO:000091019	Thyroid	PTC	cytokinesis	82/5968	173/18723	1.37e-05	1.47e-04	82
GO:1902904111	Thyroid	PTC	negative regulation of supramolecular fiber organization	78/5968	167/18723	4.16e-05	3.80e-04	78
GO:00328866	Thyroid	PTC	regulation of microtubule-based process	105/5968	240/18723	6.91e-05	6.03e-04	105
GO:00616408	Thyroid	PTC	cytoskeleton-dependent cytokinesis	50/5968	100/18723	1.20e-04	9.59e-04	50
GO:00436247	Thyroid	PTC	cellular protein complex disassembly	64/5968	136/18723	1.49e-04	1.15e-03	64
GO:00311105	Thyroid	PTC	regulation of microtubule polymerization or depolymerization	44/5968	88/18723	3.00e-04	2.11e-03	44

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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

CKAP2

SNV

Missense_Mutation

novel

c.1303N>G

p.Asn435Asp

p.N435D

Q8WWK9

protein_coding

tolerated(0.13)

possibly_damaging(0.616)

TCGA-A2-A0CP-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CKAP2

SNV

Missense_Mutation

rs775705785

c.383C>T

p.Pro128Leu

p.P128L

Q8WWK9

protein_coding

tolerated(1)

benign(0)

TCGA-A2-A3KC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CKAP2

SNV

Missense_Mutation

novel

c.1739C>A

p.Pro580His

p.P580H

Q8WWK9

protein_coding

deleterious(0)

probably_damaging(0.983)

TCGA-A8-A07J-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

5-fluorouracil

CKAP2

SNV

Missense_Mutation

novel

c.304N>T

p.Pro102Ser

p.P102S

Q8WWK9

protein_coding

tolerated(0.16)

probably_damaging(0.998)

TCGA-AO-A0JC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

CKAP2

SNV

Missense_Mutation

c.1914N>T

p.Leu638Phe

p.L638F

Q8WWK9

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-AQ-A0Y5-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

cytoxan

CKAP2

SNV

Missense_Mutation

c.638N>A

p.Pro213His

p.P213H

Q8WWK9

protein_coding

deleterious(0.04)

possibly_damaging(0.724)

TCGA-BH-A0C0-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

CKAP2

SNV

Missense_Mutation

novel

c.1390T>C

p.Trp464Arg

p.W464R

Q8WWK9

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-BH-A0HA-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CKAP2

SNV

Missense_Mutation

c.1658N>G

p.Leu553Arg

p.L553R

Q8WWK9

protein_coding

tolerated(0.46)

benign(0)

TCGA-C8-A133-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

CKAP2

SNV

Missense_Mutation

c.1516N>G

p.Leu506Val

p.L506V

Q8WWK9

protein_coding

deleterious(0.01)

benign(0.415)

TCGA-C8-A26V-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Hormone Therapy

tamoxiphen

CKAP2

SNV

Missense_Mutation

novel

c.902A>G

p.Lys301Arg

p.K301R

Q8WWK9

protein_coding

deleterious(0.03)

possibly_damaging(0.864)

TCGA-S3-AA11-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

letrozole

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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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