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: TRAPPC9

Gene summary for TRAPPC9

Gene summary.

Gene information	Species	Human
	Gene symbol	TRAPPC9
	Gene ID	83696
	Gene name	trafficking protein particle complex subunit 9
	Gene Alias	IBP
	Cytomap	8q24.3
	Gene Type	protein-coding
	GO ID	GO:0006139
	UniProtAcc	Q96Q05

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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
83696	TRAPPC9	CCI_1	Human	Cervix	CC	5.73e-10	8.66e-01	0.528
83696	TRAPPC9	CCI_2	Human	Cervix	CC	4.71e-14	1.35e+00	0.5249
83696	TRAPPC9	CCI_3	Human	Cervix	CC	4.71e-12	1.11e+00	0.516
83696	TRAPPC9	CCII_1	Human	Cervix	CC	2.30e-05	3.75e-01	0.3249
83696	TRAPPC9	HTA11_3410_2000001011	Human	Colorectum	AD	9.97e-19	-6.43e-01	0.0155
83696	TRAPPC9	HTA11_3361_2000001011	Human	Colorectum	AD	1.50e-02	-4.10e-01	-0.1207
83696	TRAPPC9	HTA11_7862_2000001011	Human	Colorectum	AD	9.50e-03	-4.48e-01	-0.0179
83696	TRAPPC9	HTA11_866_3004761011	Human	Colorectum	AD	2.41e-05	-4.62e-01	0.096
83696	TRAPPC9	HTA11_99999970781_79442	Human	Colorectum	MSS	3.62e-12	-5.28e-01	0.294
83696	TRAPPC9	HTA11_99999965104_69814	Human	Colorectum	MSS	6.08e-05	5.94e-01	0.281
83696	TRAPPC9	F007	Human	Colorectum	FAP	2.32e-04	-2.14e-01	0.1176
83696	TRAPPC9	A002-C-010	Human	Colorectum	FAP	1.75e-02	-8.56e-02	0.242
83696	TRAPPC9	A001-C-207	Human	Colorectum	FAP	1.86e-05	-2.58e-01	0.1278
83696	TRAPPC9	A015-C-203	Human	Colorectum	FAP	1.62e-35	-6.29e-01	-0.1294
83696	TRAPPC9	A015-C-204	Human	Colorectum	FAP	9.57e-10	-3.67e-01	-0.0228
83696	TRAPPC9	A014-C-040	Human	Colorectum	FAP	1.88e-07	-2.26e-01	-0.1184
83696	TRAPPC9	A002-C-201	Human	Colorectum	FAP	1.14e-16	-3.48e-01	0.0324
83696	TRAPPC9	A001-C-119	Human	Colorectum	FAP	3.74e-11	-3.71e-01	-0.1557
83696	TRAPPC9	A001-C-108	Human	Colorectum	FAP	6.28e-13	-2.96e-01	-0.0272
83696	TRAPPC9	A002-C-205	Human	Colorectum	FAP	2.65e-30	-3.10e-01	-0.1236

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
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
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

∗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:00510904	Cervix	CC	regulation of DNA-binding transcription factor activity	87/2311	440/18723	4.85e-06	1.22e-04	87
GO:00510915	Cervix	CC	positive regulation of DNA-binding transcription factor activity	51/2311	260/18723	5.05e-04	4.92e-03	51
GO:00510923	Cervix	CC	positive regulation of NF-kappaB transcription factor activity	32/2311	152/18723	1.62e-03	1.25e-02	32
GO:00219873	Cervix	CC	cerebral cortex development	25/2311	114/18723	2.81e-03	1.88e-02	25
GO:00309003	Cervix	CC	forebrain development	64/2311	379/18723	5.53e-03	3.19e-02	64
GO:00215433	Cervix	CC	pallium development	32/2311	169/18723	8.73e-03	4.48e-02	32
GO:0051091	Colorectum	AD	positive regulation of DNA-binding transcription factor activity	73/3918	260/18723	3.52e-03	2.54e-02	73
GO:00510912	Colorectum	MSS	positive regulation of DNA-binding transcription factor activity	69/3467	260/18723	8.44e-04	8.71e-03	69
GO:0051090	Colorectum	MSS	regulation of DNA-binding transcription factor activity	106/3467	440/18723	1.88e-03	1.65e-02	106
GO:0021987	Colorectum	FAP	cerebral cortex development	28/2622	114/18723	1.80e-03	1.55e-02	28
GO:0021543	Colorectum	FAP	pallium development	36/2622	169/18723	6.06e-03	3.81e-02	36
GO:00510901	Colorectum	FAP	regulation of DNA-binding transcription factor activity	80/2622	440/18723	7.90e-03	4.67e-02	80
GO:0030900	Colorectum	FAP	forebrain development	70/2622	379/18723	8.64e-03	4.98e-02	70
GO:00309001	Colorectum	CRC	forebrain development	66/2078	379/18723	1.36e-04	2.57e-03	66
GO:00219871	Colorectum	CRC	cerebral cortex development	24/2078	114/18723	1.45e-03	1.57e-02	24
GO:00215431	Colorectum	CRC	pallium development	32/2078	169/18723	1.74e-03	1.79e-02	32
GO:0021537	Colorectum	CRC	telencephalon development	43/2078	248/18723	2.01e-03	2.01e-02	43
GO:00510905	Endometrium	AEH	regulation of DNA-binding transcription factor activity	69/2100	440/18723	2.51e-03	1.87e-02	69
GO:005109013	Endometrium	EEC	regulation of DNA-binding transcription factor activity	75/2168	440/18723	3.71e-04	3.97e-03	75
GO:00219874	Endometrium	EEC	cerebral cortex development	23/2168	114/18723	5.41e-03	3.32e-02	23

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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

TRAPPC9

SNV

Missense_Mutation

novel

c.2367N>G

p.Ile789Met

p.I789M

Q96Q05

protein_coding

deleterious(0)

probably_damaging(0.935)

TCGA-A2-A0SU-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

arimidex

TRAPPC9

SNV

Missense_Mutation

rs150200902

c.3469N>A

p.Ala1157Thr

p.A1157T

Q96Q05

protein_coding

tolerated(0.8)

possibly_damaging(0.714)

TCGA-A7-A26G-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

TRAPPC9

SNV

Missense_Mutation

rs750167029

c.3572N>T

p.Ala1191Val

p.A1191V

Q96Q05

protein_coding

tolerated(0.28)

benign(0.062)

TCGA-AC-A8OP-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

TRAPPC9

SNV

Missense_Mutation

rs145782440

c.1471N>A

p.Glu491Lys

p.E491K

Q96Q05

protein_coding

deleterious(0.01)

possibly_damaging(0.506)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

TRAPPC9

SNV

Missense_Mutation

c.2752N>A

p.Leu918Met

p.L918M

Q96Q05

protein_coding

tolerated(0.19)

possibly_damaging(0.584)

TCGA-AO-A128-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

TRAPPC9

SNV

Missense_Mutation

c.1226N>A

p.Ile409Asn

p.I409N

Q96Q05

protein_coding

tolerated(0.07)

possibly_damaging(0.538)

TCGA-BH-A209-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

TRAPPC9

SNV

Missense_Mutation

c.2092N>A

p.Glu698Lys

p.E698K

Q96Q05

protein_coding

deleterious(0)

possibly_damaging(0.81)

TCGA-D8-A1JA-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

adriamycin

TRAPPC9

SNV

Missense_Mutation

c.1186C>T

p.Leu396Phe

p.L396F

Q96Q05

protein_coding

deleterious(0.04)

probably_damaging(0.954)

TCGA-EW-A1OV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

epirubicin

TRAPPC9

SNV

Missense_Mutation

novel

c.116N>T

p.Ala39Val

p.A39V

Q96Q05

protein_coding

deleterious_low_confidence(0)

benign(0)

TCGA-GM-A3XL-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

fluorouracil

TRAPPC9

insertion

In_Frame_Ins

novel

c.1903_1904insCACACGGGAACAGGGCAGCTCCTCGCCCACACAAGCACT

p.Leu635delinsProHisGlyAsnArgAlaAlaProArgProHisLysHisPhe

p.L635delinsPHGNRAAPRPHKHF

Q96Q05

protein_coding

TCGA-A2-A0EQ-01

Breast

breast invasive carcinoma

Female

<65

I/II

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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