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: COL13A1

Gene summary for COL13A1

Gene summary.

Gene information	Species	Human
	Gene symbol	COL13A1
	Gene ID	1305
	Gene name	collagen type XIII alpha 1 chain
	Gene Alias	CMS19
	Cytomap	10q22.1
	Gene Type	protein-coding
	GO ID	GO:0001501
	UniProtAcc	Q5TAT6

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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
1305	COL13A1	PTC01	Human	Thyroid	PTC	1.09e-02	1.18e-01	0.1899
1305	COL13A1	PTC04	Human	Thyroid	PTC	1.09e-02	9.16e-02	0.1927
1305	COL13A1	PTC06	Human	Thyroid	PTC	1.69e-04	1.82e-01	0.2057
1305	COL13A1	PTC07	Human	Thyroid	PTC	1.04e-12	2.75e-01	0.2044
1305	COL13A1	ATC11	Human	Thyroid	ATC	2.49e-06	5.38e-01	0.3386
1305	COL13A1	ATC3	Human	Thyroid	ATC	5.52e-09	5.41e-01	0.338

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
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:0031589111	Thyroid	PTC	cell-substrate adhesion	169/5968	363/18723	2.73e-09	7.57e-08	169
GO:0001503110	Thyroid	PTC	ossification	176/5968	408/18723	9.26e-07	1.40e-05	176
GO:000716020	Thyroid	PTC	cell-matrix adhesion	109/5968	233/18723	1.28e-06	1.84e-05	109
GO:00603486	Thyroid	PTC	bone development	90/5968	205/18723	1.89e-04	1.42e-03	90
GO:00301986	Thyroid	PTC	extracellular matrix organization	124/5968	301/18723	3.75e-04	2.53e-03	124
GO:00430626	Thyroid	PTC	extracellular structure organization	124/5968	302/18723	4.38e-04	2.92e-03	124
GO:00452296	Thyroid	PTC	external encapsulating structure organization	124/5968	304/18723	5.96e-04	3.79e-03	124
GO:000176316	Thyroid	PTC	morphogenesis of a branching structure	81/5968	196/18723	3.20e-03	1.57e-02	81
GO:00301995	Thyroid	PTC	collagen fibril organization	29/5968	61/18723	7.57e-03	3.23e-02	29
GO:003158928	Thyroid	ATC	cell-substrate adhesion	195/6293	363/18723	1.58e-15	1.17e-13	195
GO:000150332	Thyroid	ATC	ossification	206/6293	408/18723	9.23e-13	3.95e-11	206
GO:0007160111	Thyroid	ATC	cell-matrix adhesion	128/6293	233/18723	1.49e-11	5.41e-10	128
GO:003019812	Thyroid	ATC	extracellular matrix organization	152/6293	301/18723	8.63e-10	2.24e-08	152
GO:004306212	Thyroid	ATC	extracellular structure organization	152/6293	302/18723	1.17e-09	2.94e-08	152
GO:004522912	Thyroid	ATC	external encapsulating structure organization	152/6293	304/18723	2.11e-09	5.08e-08	152
GO:003019911	Thyroid	ATC	collagen fibril organization	43/6293	61/18723	4.24e-09	9.57e-08	43
GO:006034813	Thyroid	ATC	bone development	102/6293	205/18723	1.18e-06	1.52e-05	102
GO:000176317	Thyroid	ATC	morphogenesis of a branching structure	96/6293	196/18723	5.68e-06	6.04e-05	96
GO:0060349	Thyroid	ATC	bone morphogenesis	50/6293	93/18723	4.87e-05	3.88e-04	50
GO:00487053	Thyroid	ATC	skeletal system morphogenesis	101/6293	220/18723	9.48e-05	6.93e-04	101

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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

COL13A1

SNV

Missense_Mutation

rs371347973

c.1505G>A

p.Arg502His

p.R502H

Q5TAT6

protein_coding

deleterious(0)

probably_damaging(0.996)

TCGA-AN-A0FJ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

COL13A1

SNV

Missense_Mutation

c.280N>G

p.Gln94Glu

p.Q94E

Q5TAT6

protein_coding

deleterious_low_confidence(0.02)

benign(0.188)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

COL13A1

SNV

Missense_Mutation

c.1959N>A

p.Met653Ile

p.M653I

Q5TAT6

protein_coding

tolerated(0.43)

benign(0.006)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

COL13A1

insertion

Frame_Shift_Ins

novel

c.1866_1867insGGGCAGAGTCTTGACGGCTTTGTAGG

p.Arg623GlyfsTer40

p.R623Gfs*40

Q5TAT6

protein_coding

TCGA-AO-A0JD-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

COL13A1

SNV

Missense_Mutation

novel

c.1492G>A

p.Glu498Lys

p.E498K

Q5TAT6

protein_coding

deleterious(0.03)

benign(0.422)

TCGA-EA-A3HS-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

COL13A1

SNV

Missense_Mutation

c.2051N>C

p.Arg684Thr

p.R684T

Q5TAT6

protein_coding

tolerated(0.11)

probably_damaging(0.994)

TCGA-EK-A2R8-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

COL13A1

SNV

Missense_Mutation

rs755589502

c.232N>C

p.Glu78Gln

p.E78Q

Q5TAT6

protein_coding

tolerated_low_confidence(0.22)

benign(0.054)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

COL13A1

SNV

Missense_Mutation

c.325N>A

p.Glu109Lys

p.E109K

Q5TAT6

protein_coding

deleterious_low_confidence(0.02)

benign(0.057)

TCGA-JX-A3Q0-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Unknown

COL13A1

SNV

Missense_Mutation

novel

c.862G>C

p.Gly288Arg

p.G288R

Q5TAT6

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-MA-AA3X-01

Cervix

cervical & endocervical cancer

Female

<65

III/IV

Chemotherapy

cisplatin

COL13A1

SNV

Missense_Mutation

c.428G>A

p.Gly143Glu

p.G143E

Q5TAT6

protein_coding

deleterious(0)

probably_damaging(0.998)

TCGA-MU-A51Y-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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