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: NUDC

Gene summary for NUDC

Gene summary.

Gene information	Species	Human
	Gene symbol	NUDC
	Gene ID	10726
	Gene name	nuclear distribution C, dynein complex regulator
	Gene Alias	HNUDC
	Cytomap	1p36.11
	Gene Type	protein-coding
	GO ID	GO:0000070
	UniProtAcc	Q9Y266

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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
10726	NUDC	GSM4909282	Human	Breast	IDC	1.52e-10	3.89e-01	-0.0288
10726	NUDC	GSM4909296	Human	Breast	IDC	8.44e-06	-9.34e-02	0.1524
10726	NUDC	GSM4909297	Human	Breast	IDC	1.88e-11	-2.62e-02	0.1517
10726	NUDC	GSM4909311	Human	Breast	IDC	1.98e-27	-3.98e-01	0.1534
10726	NUDC	GSM4909312	Human	Breast	IDC	6.43e-11	-2.79e-01	0.1552
10726	NUDC	GSM4909318	Human	Breast	IDC	2.85e-02	1.66e-01	0.2031
10726	NUDC	GSM4909319	Human	Breast	IDC	4.13e-39	-1.78e-01	0.1563
10726	NUDC	GSM4909320	Human	Breast	IDC	3.51e-06	-1.28e-01	0.1575
10726	NUDC	GSM4909321	Human	Breast	IDC	1.76e-11	5.69e-02	0.1559
10726	NUDC	brca1	Human	Breast	Precancer	9.31e-18	5.35e-01	-0.0338
10726	NUDC	brca2	Human	Breast	Precancer	1.72e-17	4.43e-01	-0.024
10726	NUDC	brca3	Human	Breast	Precancer	8.92e-10	3.89e-01	-0.0263
10726	NUDC	M2	Human	Breast	IDC	8.04e-03	8.61e-02	0.21
10726	NUDC	NCCBC11	Human	Breast	DCIS	2.15e-02	1.75e-01	0.1232
10726	NUDC	NCCBC14	Human	Breast	DCIS	1.52e-11	-7.65e-03	0.2021
10726	NUDC	NCCBC2	Human	Breast	DCIS	5.86e-03	-2.00e-01	0.1554
10726	NUDC	NCCBC5	Human	Breast	DCIS	4.01e-14	-2.16e-04	0.2046
10726	NUDC	P1	Human	Breast	IDC	2.89e-25	-2.72e-01	0.1527
10726	NUDC	P2	Human	Breast	IDC	3.28e-14	5.17e-01	0.21
10726	NUDC	DCIS2	Human	Breast	DCIS	2.23e-61	1.95e-01	0.0085

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
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
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:000645710	Endometrium	AEH	protein folding	61/2100	212/18723	1.86e-12	3.48e-10	61
GO:00516568	Endometrium	AEH	establishment of organelle localization	77/2100	390/18723	4.89e-07	1.94e-05	77
GO:19028504	Endometrium	AEH	microtubule cytoskeleton organization involved in mitosis	28/2100	147/18723	3.46e-03	2.39e-02	28
GO:00070524	Endometrium	AEH	mitotic spindle organization	23/2100	120/18723	7.01e-03	4.07e-02	23
GO:000645715	Endometrium	EEC	protein folding	63/2168	212/18723	6.82e-13	1.40e-10	63
GO:005165613	Endometrium	EEC	establishment of organelle localization	75/2168	390/18723	6.23e-06	1.49e-04	75
GO:000645720	Esophagus	HGIN	protein folding	75/2587	212/18723	1.61e-15	3.86e-13	75
GO:005165616	Esophagus	HGIN	establishment of organelle localization	90/2587	390/18723	4.27e-07	1.94e-05	90
GO:00500003	Esophagus	HGIN	chromosome localization	24/2587	82/18723	2.07e-04	3.82e-03	24
GO:00070527	Esophagus	HGIN	mitotic spindle organization	31/2587	120/18723	3.35e-04	5.50e-03	31
GO:01400146	Esophagus	HGIN	mitotic nuclear division	61/2587	287/18723	3.38e-04	5.55e-03	61
GO:00070593	Esophagus	HGIN	chromosome segregation	71/2587	346/18723	3.47e-04	5.62e-03	71
GO:19028507	Esophagus	HGIN	microtubule cytoskeleton organization involved in mitosis	36/2587	147/18723	3.61e-04	5.68e-03	36
GO:00513033	Esophagus	HGIN	establishment of chromosome localization	23/2587	80/18723	3.71e-04	5.77e-03	23
GO:00070518	Esophagus	HGIN	spindle organization	42/2587	184/18723	6.07e-04	8.49e-03	42
GO:00070803	Esophagus	HGIN	mitotic metaphase plate congression	15/2587	50/18723	2.35e-03	2.39e-02	15
GO:00513103	Esophagus	HGIN	metaphase plate congression	18/2587	65/18723	2.46e-03	2.45e-02	18
GO:00000703	Esophagus	HGIN	mitotic sister chromatid segregation	36/2587	168/18723	4.42e-03	3.87e-02	36
GO:014001414	Esophagus	ESCC	mitotic nuclear division	218/8552	287/18723	6.17e-26	1.78e-23	218
GO:005165617	Esophagus	ESCC	establishment of organelle localization	273/8552	390/18723	9.13e-23	1.81e-20	273

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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

NUDC

insertion

Frame_Shift_Ins

novel

c.267_268insAAGCATCACTTTTTAAAACAGCCAGTTTATTG

p.Arg90LysfsTer11

p.R90Kfs*11

Q9Y266

protein_coding

TCGA-A2-A0CM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

adriamycin

NUDC

insertion

Nonsense_Mutation

novel

c.557_558insCAAGATGGTGAAACCCCATCTCTACTAAAAATACAAAAA

p.Pro186_Phe187insLysMetValLysProHisLeuTyrTerLysTyrLysAsn

p.P186_F187insKMVKPHLY*KYKN

Q9Y266

protein_coding

TCGA-B6-A0I9-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unknown

NUDC

insertion

Nonsense_Mutation

novel

c.613_614insATCTCTACTAAAAATACAAAAATTAGCCA

p.Arg205HisfsTer4

p.R205Hfs*4

Q9Y266

protein_coding

TCGA-B6-A0RE-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

NUDC

SNV

Missense_Mutation

novel

c.743N>C

p.Ile248Thr

p.I248T

Q9Y266

protein_coding

deleterious(0.03)

benign(0.036)

TCGA-C5-A2LV-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

NUDC

SNV

Missense_Mutation

novel

c.814N>A

p.Glu272Lys

p.E272K

Q9Y266

protein_coding

deleterious(0)

probably_damaging(0.987)

TCGA-VS-A8EL-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

NUDC

SNV

Missense_Mutation

rs556308052

c.130N>G

p.Ile44Val

p.I44V

Q9Y266

protein_coding

tolerated(0.29)

benign(0.003)

TCGA-A6-6780-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Unknown

NUDC

SNV

Missense_Mutation

c.344N>G

p.Leu115Arg

p.L115R

Q9Y266

protein_coding

deleterious(0.02)

probably_damaging(0.977)

TCGA-AD-6889-01

Colorectum

colon adenocarcinoma

Male

>=65

I/II

Chemotherapy

xeloda

NUDC

SNV

Missense_Mutation

c.484N>G

p.Asn162Asp

p.N162D

Q9Y266

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-AZ-6598-01

Colorectum

colon adenocarcinoma

Female

>=65

I/II

Unknown

NUDC

SNV

Missense_Mutation

c.911C>T

p.Ser304Leu

p.S304L

Q9Y266

protein_coding

deleterious(0)

probably_damaging(0.995)

TCGA-AG-4015-01

Colorectum

rectum adenocarcinoma

Female

>=65

I/II

Unknown

NUDC

SNV

Missense_Mutation

rs757295638

c.916N>A

p.Glu306Lys

p.E306K

Q9Y266

protein_coding

deleterious(0)

probably_damaging(0.943)

TCGA-A5-A0G2-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

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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