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: CC2D1A

Gene summary for CC2D1A

Gene summary.

Gene information	Species	Human
	Gene symbol	CC2D1A
	Gene ID	54862
	Gene name	coiled-coil and C2 domain containing 1A
	Gene Alias	Aki-1
	Cytomap	19p13.12
	Gene Type	protein-coding
	GO ID	GO:0000122
	UniProtAcc	Q6P1N0

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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
54862	CC2D1A	HTA11_1391_2000001011	Human	Colorectum	AD	5.61e-03	4.58e-01	-0.059
54862	CC2D1A	HTA11_546_2000001011	Human	Colorectum	AD	7.97e-03	4.14e-01	-0.0842
54862	CC2D1A	HTA11_10711_2000001011	Human	Colorectum	AD	2.01e-03	4.43e-01	0.0338
54862	CC2D1A	HTA11_7696_3000711011	Human	Colorectum	AD	1.07e-10	6.04e-01	0.0674
54862	CC2D1A	A015-C-203	Human	Colorectum	FAP	1.06e-12	4.26e-02	-0.1294
54862	CC2D1A	A002-C-201	Human	Colorectum	FAP	6.42e-03	-4.92e-02	0.0324
54862	CC2D1A	A001-C-108	Human	Colorectum	FAP	2.37e-05	-9.27e-02	-0.0272
54862	CC2D1A	A002-C-205	Human	Colorectum	FAP	7.69e-09	-2.46e-01	-0.1236
54862	CC2D1A	A015-C-006	Human	Colorectum	FAP	7.24e-05	-4.65e-02	-0.0994
54862	CC2D1A	A015-C-106	Human	Colorectum	FAP	2.17e-04	2.72e-04	-0.0511
54862	CC2D1A	A002-C-114	Human	Colorectum	FAP	1.85e-05	-2.68e-02	-0.1561
54862	CC2D1A	A015-C-104	Human	Colorectum	FAP	1.90e-12	-2.86e-02	-0.1899
54862	CC2D1A	A001-C-014	Human	Colorectum	FAP	1.63e-03	-1.42e-01	0.0135
54862	CC2D1A	A002-C-016	Human	Colorectum	FAP	2.01e-10	-2.26e-01	0.0521
54862	CC2D1A	A015-C-002	Human	Colorectum	FAP	5.12e-04	-2.27e-01	-0.0763
54862	CC2D1A	A001-C-203	Human	Colorectum	FAP	1.88e-05	-8.55e-02	-0.0481
54862	CC2D1A	A002-C-116	Human	Colorectum	FAP	2.75e-12	-2.95e-01	-0.0452
54862	CC2D1A	A014-C-008	Human	Colorectum	FAP	8.25e-04	-1.80e-01	-0.191
54862	CC2D1A	A018-E-020	Human	Colorectum	FAP	1.45e-07	-2.19e-01	-0.2034
54862	CC2D1A	F034	Human	Colorectum	FAP	1.90e-07	-1.66e-01	-0.0665

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
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
Esophagus	ESCC
Skin	AK
Skin	SCCIS
Skin	cSCC
Thyroid	HT

∗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:0043123	Colorectum	AD	positive regulation of I-kappaB kinase/NF-kappaB signaling	60/3918	186/18723	1.91e-04	2.56e-03	60
GO:0043122	Colorectum	AD	regulation of I-kappaB kinase/NF-kappaB signaling	76/3918	249/18723	2.17e-04	2.85e-03	76
GO:0007249	Colorectum	AD	I-kappaB kinase/NF-kappaB signaling	82/3918	281/18723	6.09e-04	6.40e-03	82
GO:00431222	Colorectum	FAP	regulation of I-kappaB kinase/NF-kappaB signaling	56/2622	249/18723	1.82e-04	2.69e-03	56
GO:00431232	Colorectum	FAP	positive regulation of I-kappaB kinase/NF-kappaB signaling	42/2622	186/18723	1.01e-03	9.89e-03	42
GO:00072492	Colorectum	FAP	I-kappaB kinase/NF-kappaB signaling	58/2622	281/18723	1.37e-03	1.24e-02	58
GO:00431223	Colorectum	CRC	regulation of I-kappaB kinase/NF-kappaB signaling	41/2078	249/18723	6.39e-03	4.64e-02	41
GO:004312220	Esophagus	HGIN	regulation of I-kappaB kinase/NF-kappaB signaling	63/2587	249/18723	8.91e-07	3.61e-05	63
GO:000724918	Esophagus	HGIN	I-kappaB kinase/NF-kappaB signaling	67/2587	281/18723	3.84e-06	1.29e-04	67
GO:004312317	Esophagus	HGIN	positive regulation of I-kappaB kinase/NF-kappaB signaling	49/2587	186/18723	4.22e-06	1.40e-04	49
GO:004312318	Esophagus	ESCC	positive regulation of I-kappaB kinase/NF-kappaB signaling	132/8552	186/18723	2.07e-12	8.58e-11	132
GO:0043122110	Esophagus	ESCC	regulation of I-kappaB kinase/NF-kappaB signaling	167/8552	249/18723	6.11e-12	2.32e-10	167
GO:000724919	Esophagus	ESCC	I-kappaB kinase/NF-kappaB signaling	183/8552	281/18723	3.02e-11	1.01e-09	183
GO:00987812	Esophagus	ESCC	ncRNA transcription	45/8552	56/18723	1.05e-07	1.72e-06	45
GO:00093011	Esophagus	ESCC	snRNA transcription	16/8552	19/18723	6.45e-04	3.43e-03	16
GO:00427951	Esophagus	ESCC	snRNA transcription by RNA polymerase II	13/8552	16/18723	4.05e-03	1.62e-02	13
GO:004312218	Oral cavity	OSCC	regulation of I-kappaB kinase/NF-kappaB signaling	155/7305	249/18723	7.79e-14	4.14e-12	155
GO:004312310	Oral cavity	OSCC	positive regulation of I-kappaB kinase/NF-kappaB signaling	122/7305	186/18723	1.68e-13	8.52e-12	122
GO:000724910	Oral cavity	OSCC	I-kappaB kinase/NF-kappaB signaling	169/7305	281/18723	4.69e-13	2.25e-11	169
GO:00987811	Oral cavity	OSCC	ncRNA transcription	38/7305	56/18723	1.15e-05	1.18e-04	38

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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

CC2D1A

SNV

Missense_Mutation

c.593N>A

p.Gly198Glu

p.G198E

Q6P1N0

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A2-A0YK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CC2D1A

SNV

Missense_Mutation

rs747172992

c.1762G>A

p.Glu588Lys

p.E588K

Q6P1N0

protein_coding

deleterious(0.04)

possibly_damaging(0.711)

TCGA-B6-A0IK-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

CC2D1A

SNV

Missense_Mutation

rs750684031

c.1081N>C

p.Val361Leu

p.V361L

Q6P1N0

protein_coding

tolerated(0.29)

benign(0.007)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

CC2D1A

SNV

Missense_Mutation

c.1630N>C

p.Asp544His

p.D544H

Q6P1N0

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-D8-A1XZ-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen+anastrozolum

CC2D1A

SNV

Missense_Mutation

novel

c.1064G>A

p.Arg355Gln

p.R355Q

Q6P1N0

protein_coding

deleterious(0.01)

probably_damaging(0.996)

TCGA-E2-A574-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CC2D1A

SNV

Missense_Mutation

novel

c.1342G>A

p.Glu448Lys

p.E448K

Q6P1N0

protein_coding

tolerated(0.13)

possibly_damaging(0.815)

TCGA-E2-A574-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CC2D1A

SNV

Missense_Mutation

c.2752N>A

p.Glu918Lys

p.E918K

Q6P1N0

protein_coding

deleterious(0)

possibly_damaging(0.777)

TCGA-EW-A1J5-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

CC2D1A

insertion

Nonsense_Mutation

novel

c.2557_2558insAGGCTTCTCTCTCCCTACTCCCTCCTGTGGTTCATGTCCATGAA

p.Phe853Ter

p.F853*

Q6P1N0

protein_coding

TCGA-A2-A0CU-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

tamoxiphen

CC2D1A

SNV

Missense_Mutation

c.2788N>A

p.Asp930Asn

p.D930N

Q6P1N0

protein_coding

deleterious(0)

benign(0.147)

TCGA-C5-A1BM-01

Cervix

cervical & endocervical cancer

Female

>=65

I/II

Unknown

CC2D1A

SNV

Missense_Mutation

novel

c.464G>T

p.Arg155Ile

p.R155I

Q6P1N0

protein_coding

deleterious(0)

benign(0.259)

TCGA-EA-A3HU-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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