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: OCIAD2

Gene summary for OCIAD2

Gene summary.

Gene information	Species	Human
	Gene symbol	OCIAD2
	Gene ID	132299
	Gene name	OCIA domain containing 2
	Gene Alias	OCIAD2
	Cytomap	4p11
	Gene Type	protein-coding
	GO ID	GO:0006810
	UniProtAcc	Q56VL3

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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
132299	OCIAD2	HTA11_2487_2000001011	Human	Colorectum	SER	4.37e-17	1.04e+00	-0.1808
132299	OCIAD2	HTA11_1938_2000001011	Human	Colorectum	AD	7.95e-19	1.11e+00	-0.0811
132299	OCIAD2	HTA11_78_2000001011	Human	Colorectum	AD	2.41e-04	4.27e-01	-0.1088
132299	OCIAD2	HTA11_347_2000001011	Human	Colorectum	AD	9.86e-11	4.62e-01	-0.1954
132299	OCIAD2	HTA11_411_2000001011	Human	Colorectum	SER	2.30e-04	1.11e+00	-0.2602
132299	OCIAD2	HTA11_83_2000001011	Human	Colorectum	SER	5.17e-10	8.38e-01	-0.1526
132299	OCIAD2	HTA11_696_2000001011	Human	Colorectum	AD	1.64e-11	5.23e-01	-0.1464
132299	OCIAD2	HTA11_1391_2000001011	Human	Colorectum	AD	3.59e-11	7.95e-01	-0.059
132299	OCIAD2	HTA11_5212_2000001011	Human	Colorectum	AD	3.80e-02	5.54e-01	-0.2061
132299	OCIAD2	HTA11_7862_2000001011	Human	Colorectum	AD	3.33e-04	4.66e-01	-0.0179
132299	OCIAD2	HTA11_866_3004761011	Human	Colorectum	AD	4.98e-13	6.29e-01	0.096
132299	OCIAD2	HTA11_4255_2000001011	Human	Colorectum	SER	1.93e-04	5.49e-01	0.0446
132299	OCIAD2	HTA11_8622_2000001021	Human	Colorectum	SER	1.95e-04	4.94e-01	0.0528
132299	OCIAD2	HTA11_7696_3000711011	Human	Colorectum	AD	5.60e-16	7.09e-01	0.0674
132299	OCIAD2	HTA11_6818_2000001021	Human	Colorectum	AD	3.82e-15	8.39e-01	0.0588
132299	OCIAD2	HTA11_99999970781_79442	Human	Colorectum	MSS	3.42e-32	1.01e+00	0.294
132299	OCIAD2	HTA11_99999965104_69814	Human	Colorectum	MSS	5.87e-06	4.84e-01	0.281
132299	OCIAD2	HTA11_99999971662_82457	Human	Colorectum	MSS	1.10e-34	1.07e+00	0.3859
132299	OCIAD2	HTA11_99999973899_84307	Human	Colorectum	MSS	8.73e-05	5.74e-01	0.2585
132299	OCIAD2	HTA11_99999974143_84620	Human	Colorectum	MSS	2.14e-07	3.83e-01	0.3005

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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
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
GC		CAG: Chronic atrophic gastritis
		CAG with IM: Chronic atrophic gastritis with intestinal metaplasia
		CSG: Chronic superficial gastritis
		GC: Gastric cancer
		SIM: Severe intestinal metaplasia
		WIM: Wild intestinal metaplasia
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
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
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:0048872	Colorectum	AD	homeostasis of number of cells	87/3918	272/18723	1.16e-05	2.61e-04	87
GO:00488721	Colorectum	SER	homeostasis of number of cells	65/2897	272/18723	1.70e-04	3.19e-03	65
GO:00488722	Colorectum	MSS	homeostasis of number of cells	82/3467	272/18723	2.02e-06	6.28e-05	82
GO:004887216	Endometrium	AEH	homeostasis of number of cells	53/2100	272/18723	4.10e-05	6.99e-04	53
GO:004887217	Endometrium	EEC	homeostasis of number of cells	53/2168	272/18723	9.52e-05	1.34e-03	53
GO:0048872111	Esophagus	ESCC	homeostasis of number of cells	163/8552	272/18723	1.40e-06	1.69e-05	163
GO:004887212	Liver	Cirrhotic	homeostasis of number of cells	89/4634	272/18723	1.76e-03	1.12e-02	89
GO:004887222	Liver	HCC	homeostasis of number of cells	147/7958	272/18723	7.48e-05	6.70e-04	147
GO:004887232	Liver	Cyst	homeostasis of number of cells	16/496	272/18723	2.55e-03	4.87e-02	16
GO:00488728	Lung	IAC	homeostasis of number of cells	54/2061	272/18723	1.20e-05	3.64e-04	54
GO:004887213	Lung	AIS	homeostasis of number of cells	47/1849	272/18723	1.03e-04	2.50e-03	47
GO:004887220	Oral cavity	OSCC	homeostasis of number of cells	152/7305	272/18723	1.08e-08	2.23e-07	152
GO:0048872110	Oral cavity	LP	homeostasis of number of cells	87/4623	272/18723	3.75e-03	2.47e-02	87
GO:004887218	Prostate	BPH	homeostasis of number of cells	79/3107	272/18723	1.79e-07	3.99e-06	79
GO:004887219	Prostate	Tumor	homeostasis of number of cells	86/3246	272/18723	5.29e-09	2.11e-07	86
GO:004887228	Skin	AK	homeostasis of number of cells	56/1910	272/18723	2.33e-07	9.18e-06	56
GO:004887229	Skin	cSCC	homeostasis of number of cells	104/4864	272/18723	5.34e-06	7.71e-05	104
GO:00488726	Stomach	GC	homeostasis of number of cells	28/1159	272/18723	5.78e-03	4.42e-02	28
GO:004887211	Stomach	CAG with IM	homeostasis of number of cells	28/1050	272/18723	1.45e-03	1.65e-02	28
GO:004887221	Stomach	CSG	homeostasis of number of cells	28/1034	272/18723	1.15e-03	1.42e-02	28

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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

OCIAD2

SNV

Missense_Mutation

c.89N>T

p.Ser30Leu

p.S30L

Q56VL3

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-XX-A89A-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

OCIAD2

insertion

Frame_Shift_Ins

novel

c.344_345insGG

p.Asp115GlufsTer26

p.D115Efs*26

Q56VL3

protein_coding

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

OCIAD2

insertion

In_Frame_Ins

novel

c.342_343insAGGCAGAGAACAAGCTGGAAGTCCAGGCAGGTA

p.Glu114_Asp115insArgGlnArgThrSerTrpLysSerArgGlnVal

p.E114_D115insRQRTSWKSRQV

Q56VL3

protein_coding

TCGA-A8-A09E-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

anastrozole

OCIAD2

insertion

Frame_Shift_Ins

novel

c.397_398insA

p.Thr133AsnfsTer3

p.T133Nfs*3

Q56VL3

protein_coding

TCGA-UU-A93S-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

OCIAD2

SNV

Missense_Mutation

novel

c.366T>A

p.Phe122Leu

p.F122L

Q56VL3

protein_coding

tolerated(0.1)

probably_damaging(0.931)

TCGA-AA-A02R-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

OCIAD2

SNV

Missense_Mutation

c.268N>A

p.Ala90Thr

p.A90T

Q56VL3

protein_coding

deleterious(0.04)

probably_damaging(0.996)

TCGA-D5-6928-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

OCIAD2

SNV

Missense_Mutation

c.115A>T

p.Ile39Phe

p.I39F

Q56VL3

protein_coding

tolerated(0.08)

possibly_damaging(0.564)

TCGA-CI-6622-01

Colorectum

rectum adenocarcinoma

Male

>=65

I/II

Chemotherapy

5-fluorouracil

OCIAD2

SNV

Missense_Mutation

novel

c.370C>A

p.Pro124Thr

p.P124T

Q56VL3

protein_coding

deleterious(0)

probably_damaging(0.994)

TCGA-A5-A0G1-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

OCIAD2

SNV

Missense_Mutation

rs764161793

c.353G>A

p.Arg118His

p.R118H

Q56VL3

protein_coding

tolerated(0.57)

probably_damaging(0.997)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Unknown

OCIAD2

SNV

Missense_Mutation

rs749812067

c.123N>T

p.Lys41Asn

p.K41N

Q56VL3

protein_coding

deleterious(0.04)

probably_damaging(0.995)

TCGA-A5-A2K5-01

Endometrium

uterine corpus endometrioid carcinoma

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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