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: POM121

Gene summary for POM121

Gene summary.

Gene information	Species	Human
	Gene symbol	POM121
	Gene ID	9883
	Gene name	POM121 transmembrane nucleoporin
	Gene Alias	P145
	Cytomap	7q11.23
	Gene Type	protein-coding
	GO ID	GO:0006403
	UniProtAcc	Q96HA1

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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
9883	POM121	HTA11_347_2000001011	Human	Colorectum	AD	2.36e-04	2.62e-01	-0.1954
9883	POM121	HTA11_1391_2000001011	Human	Colorectum	AD	1.52e-02	3.61e-01	-0.059
9883	POM121	HTA11_99999971662_82457	Human	Colorectum	MSS	9.67e-09	6.90e-01	0.3859
9883	POM121	HTA11_99999974143_84620	Human	Colorectum	MSS	6.26e-10	6.36e-01	0.3005
9883	POM121	F007	Human	Colorectum	FAP	3.51e-02	-3.59e-01	0.1176
9883	POM121	A002-C-010	Human	Colorectum	FAP	2.39e-03	-2.23e-01	0.242
9883	POM121	A015-C-203	Human	Colorectum	FAP	1.52e-17	-3.43e-01	-0.1294
9883	POM121	A015-C-204	Human	Colorectum	FAP	7.00e-04	-3.19e-01	-0.0228
9883	POM121	A014-C-040	Human	Colorectum	FAP	6.53e-03	-4.07e-01	-0.1184
9883	POM121	A002-C-201	Human	Colorectum	FAP	9.61e-11	-3.55e-01	0.0324
9883	POM121	A001-C-119	Human	Colorectum	FAP	1.87e-03	-2.35e-01	-0.1557
9883	POM121	A001-C-108	Human	Colorectum	FAP	3.90e-11	-2.61e-01	-0.0272
9883	POM121	A002-C-205	Human	Colorectum	FAP	5.15e-15	-2.72e-01	-0.1236
9883	POM121	A015-C-006	Human	Colorectum	FAP	4.08e-10	-1.96e-01	-0.0994
9883	POM121	A015-C-106	Human	Colorectum	FAP	5.72e-09	-1.89e-01	-0.0511
9883	POM121	A002-C-114	Human	Colorectum	FAP	2.79e-14	-4.04e-01	-0.1561
9883	POM121	A015-C-104	Human	Colorectum	FAP	2.49e-18	-3.28e-01	-0.1899
9883	POM121	A001-C-014	Human	Colorectum	FAP	3.39e-11	-3.59e-01	0.0135
9883	POM121	A002-C-016	Human	Colorectum	FAP	2.59e-14	-3.33e-01	0.0521
9883	POM121	A015-C-002	Human	Colorectum	FAP	1.87e-07	-3.47e-01	-0.0763

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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
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
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:0072594	Colorectum	AD	establishment of protein localization to organelle	148/3918	422/18723	7.95e-12	1.04e-09	148
GO:0006913	Colorectum	AD	nucleocytoplasmic transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0051169	Colorectum	AD	nuclear transport	102/3918	301/18723	1.00e-07	4.85e-06	102
GO:0006403	Colorectum	AD	RNA localization	71/3918	201/18723	1.54e-06	4.76e-05	71
GO:0034504	Colorectum	AD	protein localization to nucleus	94/3918	290/18723	2.83e-06	8.09e-05	94
GO:0051236	Colorectum	AD	establishment of RNA localization	58/3918	166/18723	1.95e-05	4.01e-04	58
GO:0015931	Colorectum	AD	nucleobase-containing compound transport	73/3918	222/18723	2.02e-05	4.10e-04	73
GO:0050657	Colorectum	AD	nucleic acid transport	57/3918	163/18723	2.22e-05	4.39e-04	57
GO:0050658	Colorectum	AD	RNA transport	57/3918	163/18723	2.22e-05	4.39e-04	57
GO:0017038	Colorectum	AD	protein import	67/3918	206/18723	6.34e-05	1.05e-03	67
GO:0051168	Colorectum	AD	nuclear export	53/3918	154/18723	6.89e-05	1.11e-03	53
GO:0051170	Colorectum	AD	import into nucleus	53/3918	159/18723	1.76e-04	2.38e-03	53
GO:0006606	Colorectum	AD	protein import into nucleus	51/3918	155/18723	3.29e-04	3.86e-03	51
GO:0051028	Colorectum	AD	mRNA transport	42/3918	130/18723	1.57e-03	1.32e-02	42
GO:00725942	Colorectum	MSS	establishment of protein localization to organelle	139/3467	422/18723	5.75e-13	1.12e-10	139
GO:00069132	Colorectum	MSS	nucleocytoplasmic transport	99/3467	301/18723	1.35e-09	1.03e-07	99
GO:00511692	Colorectum	MSS	nuclear transport	99/3467	301/18723	1.35e-09	1.03e-07	99
GO:00345042	Colorectum	MSS	protein localization to nucleus	92/3467	290/18723	3.66e-08	1.98e-06	92
GO:00064032	Colorectum	MSS	RNA localization	69/3467	201/18723	6.33e-08	3.26e-06	69
GO:00159312	Colorectum	MSS	nucleobase-containing compound transport	70/3467	222/18723	1.92e-06	6.01e-05	70

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa05014	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050141	Colorectum	AD	Amyotrophic lateral sclerosis	164/2092	364/8465	4.28e-18	1.27e-16	8.09e-17	164
hsa050144	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050145	Colorectum	MSS	Amyotrophic lateral sclerosis	156/1875	364/8465	1.43e-19	4.62e-18	2.83e-18	156
hsa050148	Colorectum	FAP	Amyotrophic lateral sclerosis	91/1404	364/8465	1.84e-05	2.36e-04	1.44e-04	91
hsa050149	Colorectum	FAP	Amyotrophic lateral sclerosis	91/1404	364/8465	1.84e-05	2.36e-04	1.44e-04	91
hsa05014210	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0301321	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0501438	Esophagus	ESCC	Amyotrophic lateral sclerosis	266/4205	364/8465	1.31e-20	2.20e-18	1.13e-18	266
hsa0301331	Esophagus	ESCC	Nucleocytoplasmic transport	89/4205	108/8465	1.20e-12	2.37e-11	1.21e-11	89
hsa0501414	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
hsa0501415	Liver	Cirrhotic	Amyotrophic lateral sclerosis	187/2530	364/8465	1.56e-18	6.50e-17	4.01e-17	187
hsa0501422	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa03013	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81
hsa0501432	Liver	HCC	Amyotrophic lateral sclerosis	252/4020	364/8465	8.85e-18	7.41e-16	4.12e-16	252
hsa030131	Liver	HCC	Nucleocytoplasmic transport	81/4020	108/8465	4.28e-09	6.83e-08	3.80e-08	81

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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

POM121

SNV

Missense_Mutation

c.409N>A

p.Ala137Thr

p.A137T

Q96HA1

protein_coding

tolerated(1)

benign(0)

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

POM121

SNV

Missense_Mutation

c.159G>C

p.Glu53Asp

p.E53D

Q96HA1

protein_coding

tolerated(0.08)

possibly_damaging(0.795)

TCGA-BH-A0DZ-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

docetaxel

POM121

SNV

Missense_Mutation

c.2713N>A

p.Glu905Lys

p.E905K

Q96HA1

protein_coding

tolerated(0.05)

benign(0.219)

TCGA-E2-A10C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

POM121

SNV

Missense_Mutation

c.2977N>A

p.Ser993Thr

p.S993T

Q96HA1

protein_coding

tolerated_low_confidence(0.67)

benign(0.034)

TCGA-E9-A1ND-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

aromasin

POM121

SNV

Missense_Mutation

novel

c.349G>A

p.Asp117Asn

p.D117N

Q96HA1

protein_coding

deleterious(0.01)

possibly_damaging(0.691)

TCGA-PE-A5DE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

taxotere

POM121

SNV

Missense_Mutation

novel

c.2656N>T

p.Ala886Ser

p.A886S

Q96HA1

protein_coding

tolerated(0.48)

benign(0.009)

TCGA-PL-A8LZ-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

paclitaxel

POM121

insertion

Nonsense_Mutation

novel

c.151_152insACTACCAGACTTTTTAAACAGCTTTATTAAGATATAAT

p.Leu51HisfsTer6

p.L51Hfs*6

Q96HA1

protein_coding

TCGA-AO-A0J9-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphamide

POM121

SNV

Missense_Mutation

c.2836T>G

p.Phe946Val

p.F946V

Q96HA1

protein_coding

deleterious(0.01)

probably_damaging(0.994)

TCGA-FU-A3HZ-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

POM121

SNV

Missense_Mutation

novel

c.351N>G

p.Asp117Glu

p.D117E

Q96HA1

protein_coding

tolerated(0.19)

benign(0.039)

TCGA-AA-3818-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

POM121

SNV

Missense_Mutation

novel

c.1700N>T

p.Ser567Leu

p.S567L

Q96HA1

protein_coding

tolerated(0.71)

benign(0.003)

TCGA-AA-A00N-01

Colorectum

colon adenocarcinoma

Male

>=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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