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: CKAP5

Gene summary for CKAP5

Gene summary.

Gene information	Species	Human
	Gene symbol	CKAP5
	Gene ID	9793
	Gene name	cytoskeleton associated protein 5
	Gene Alias	CHTOG
	Cytomap	11p11.2
	Gene Type	protein-coding
	GO ID	GO:0000226
	UniProtAcc	Q14008

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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
9793	CKAP5	LZE2T	Human	Esophagus	ESCC	5.05e-04	8.41e-01	0.082
9793	CKAP5	LZE4T	Human	Esophagus	ESCC	2.12e-13	3.88e-01	0.0811
9793	CKAP5	LZE5T	Human	Esophagus	ESCC	1.76e-03	3.10e-01	0.0514
9793	CKAP5	LZE7T	Human	Esophagus	ESCC	3.52e-17	6.46e-01	0.0667
9793	CKAP5	LZE8T	Human	Esophagus	ESCC	1.40e-10	2.54e-01	0.067
9793	CKAP5	LZE24T	Human	Esophagus	ESCC	1.39e-12	3.74e-01	0.0596
9793	CKAP5	LZE6T	Human	Esophagus	ESCC	3.95e-03	3.44e-01	0.0845
9793	CKAP5	P1T-E	Human	Esophagus	ESCC	4.90e-04	2.25e-01	0.0875
9793	CKAP5	P2T-E	Human	Esophagus	ESCC	1.92e-34	5.98e-01	0.1177
9793	CKAP5	P4T-E	Human	Esophagus	ESCC	5.96e-12	4.55e-01	0.1323
9793	CKAP5	P5T-E	Human	Esophagus	ESCC	3.43e-13	2.53e-01	0.1327
9793	CKAP5	P8T-E	Human	Esophagus	ESCC	1.57e-18	3.56e-01	0.0889
9793	CKAP5	P9T-E	Human	Esophagus	ESCC	4.56e-16	3.21e-01	0.1131
9793	CKAP5	P10T-E	Human	Esophagus	ESCC	5.25e-19	3.65e-01	0.116
9793	CKAP5	P11T-E	Human	Esophagus	ESCC	1.70e-05	3.75e-01	0.1426
9793	CKAP5	P12T-E	Human	Esophagus	ESCC	2.00e-15	3.26e-01	0.1122
9793	CKAP5	P15T-E	Human	Esophagus	ESCC	2.72e-12	4.51e-01	0.1149
9793	CKAP5	P16T-E	Human	Esophagus	ESCC	6.18e-23	3.50e-01	0.1153
9793	CKAP5	P17T-E	Human	Esophagus	ESCC	5.37e-11	5.93e-01	0.1278
9793	CKAP5	P20T-E	Human	Esophagus	ESCC	4.60e-17	4.11e-01	0.1124

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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
Prostate		BPH: Benign Prostatic Hyperplasia
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:005123617	Esophagus	ESCC	establishment of RNA localization	134/8552	166/18723	1.23e-20	1.81e-18	134
GO:005065717	Esophagus	ESCC	nucleic acid transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:005065817	Esophagus	ESCC	RNA transport	131/8552	163/18723	6.94e-20	8.46e-18	131
GO:001593117	Esophagus	ESCC	nucleobase-containing compound transport	162/8552	222/18723	9.87e-17	7.93e-15	162
GO:190285015	Esophagus	ESCC	microtubule cytoskeleton organization involved in mitosis	116/8552	147/18723	1.25e-16	9.91e-15	116
GO:0043254111	Esophagus	ESCC	regulation of protein-containing complex assembly	278/8552	428/18723	3.81e-16	2.77e-14	278
GO:000705214	Esophagus	ESCC	mitotic spindle organization	97/8552	120/18723	2.17e-15	1.33e-13	97
GO:0031334111	Esophagus	ESCC	positive regulation of protein-containing complex assembly	166/8552	237/18723	2.06e-14	1.07e-12	166
GO:000705114	Esophagus	ESCC	spindle organization	134/8552	184/18723	5.70e-14	2.87e-12	134
GO:003298416	Esophagus	ESCC	protein-containing complex disassembly	151/8552	224/18723	3.45e-11	1.15e-09	151
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:000716320	Esophagus	ESCC	establishment or maintenance of cell polarity	143/8552	218/18723	2.05e-09	4.65e-08	143
GO:005149520	Esophagus	ESCC	positive regulation of cytoskeleton organization	147/8552	226/18723	2.93e-09	6.38e-08	147
GO:0051258111	Esophagus	ESCC	protein polymerization	183/8552	297/18723	1.94e-08	3.75e-07	183
GO:0032273111	Esophagus	ESCC	positive regulation of protein polymerization	95/8552	138/18723	2.97e-08	5.57e-07	95
GO:00705078	Esophagus	ESCC	regulation of microtubule cytoskeleton organization	99/8552	148/18723	1.43e-07	2.29e-06	99
GO:0032271111	Esophagus	ESCC	regulation of protein polymerization	143/8552	233/18723	9.21e-07	1.17e-05	143
GO:00070982	Esophagus	ESCC	centrosome cycle	85/8552	130/18723	4.41e-06	4.69e-05	85
GO:00310233	Esophagus	ESCC	microtubule organizing center organization	92/8552	143/18723	5.04e-06	5.31e-05	92

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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

CKAP5

SNV

Missense_Mutation

c.3470N>G

p.Ser1157Cys

p.S1157C

Q14008

protein_coding

deleterious(0.03)

probably_damaging(0.997)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CKAP5

SNV

Missense_Mutation

novel

c.4878G>C

p.Gln1626His

p.Q1626H

Q14008

protein_coding

tolerated(0.07)

possibly_damaging(0.556)

TCGA-A2-A3XT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cyclophosphamide

CKAP5

SNV

Missense_Mutation

c.5440G>A

p.Glu1814Lys

p.E1814K

Q14008

protein_coding

tolerated(0.19)

probably_damaging(0.98)

TCGA-A8-A09G-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Unknown

CKAP5

SNV

Missense_Mutation

c.5491G>A

p.Asp1831Asn

p.D1831N

Q14008

protein_coding

tolerated(0.06)

probably_damaging(0.989)

TCGA-AC-A2B8-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

chemo

CKAP5

SNV

Missense_Mutation

novel

c.1116N>T

p.Glu372Asp

p.E372D

Q14008

protein_coding

tolerated(0.05)

probably_damaging(0.971)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CKAP5

SNV

Missense_Mutation

c.5737C>G

p.Pro1913Ala

p.P1913A

Q14008

protein_coding

tolerated(0.64)

benign(0.015)

TCGA-AN-A0FL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CKAP5

SNV

Missense_Mutation

c.5000N>T

p.Ser1667Phe

p.S1667F

Q14008

protein_coding

deleterious(0.04)

possibly_damaging(0.603)

TCGA-AO-A0JC-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

CKAP5

SNV

Missense_Mutation

novel

c.2166N>A

p.Met722Ile

p.M722I

Q14008

protein_coding

tolerated(0.17)

benign(0)

TCGA-AR-A2LR-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CKAP5

SNV

Missense_Mutation

c.4459N>T

p.Asp1487Tyr

p.D1487Y

Q14008

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-B6-A0RS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

CKAP5

SNV

Missense_Mutation

c.42N>C

p.Gln14His

p.Q14H

Q14008

protein_coding

deleterious(0.01)

probably_damaging(0.964)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

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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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