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: CARMIL1

Gene summary for CARMIL1

Gene summary.

Gene information	Species	Human
	Gene symbol	CARMIL1
	Gene ID	55604
	Gene name	capping protein regulator and myosin 1 linker 1
	Gene Alias	CARMIL
	Cytomap	6p22.2
	Gene Type	protein-coding
	GO ID	GO:0000902
	UniProtAcc	Q5VZK9

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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
55604	CARMIL1	CCI_1	Human	Cervix	CC	1.32e-18	1.34e+00	0.528
55604	CARMIL1	CCI_2	Human	Cervix	CC	7.71e-10	7.94e-01	0.5249
55604	CARMIL1	CCI_3	Human	Cervix	CC	1.18e-28	1.48e+00	0.516
55604	CARMIL1	CCII_1	Human	Cervix	CC	5.19e-05	4.20e-01	0.3249
55604	CARMIL1	sample3	Human	Cervix	CC	5.84e-06	2.61e-01	0.1387
55604	CARMIL1	T3	Human	Cervix	CC	3.60e-08	2.41e-01	0.1389
55604	CARMIL1	HTA11_3410_2000001011	Human	Colorectum	AD	1.76e-20	-6.16e-01	0.0155
55604	CARMIL1	HTA11_2951_2000001011	Human	Colorectum	AD	1.12e-04	-7.32e-01	0.0216
55604	CARMIL1	HTA11_347_2000001011	Human	Colorectum	AD	2.74e-13	6.76e-01	-0.1954
55604	CARMIL1	HTA11_3361_2000001011	Human	Colorectum	AD	2.89e-04	-4.98e-01	-0.1207
55604	CARMIL1	HTA11_696_2000001011	Human	Colorectum	AD	2.89e-02	-2.72e-01	-0.1464
55604	CARMIL1	HTA11_546_2000001011	Human	Colorectum	AD	4.29e-04	-3.91e-01	-0.0842
55604	CARMIL1	HTA11_866_3004761011	Human	Colorectum	AD	1.38e-11	-5.49e-01	0.096
55604	CARMIL1	HTA11_10623_2000001011	Human	Colorectum	AD	4.37e-06	-3.50e-01	-0.0177
55604	CARMIL1	HTA11_10711_2000001011	Human	Colorectum	AD	3.10e-06	-5.31e-01	0.0338
55604	CARMIL1	HTA11_7696_3000711011	Human	Colorectum	AD	1.61e-20	-5.60e-01	0.0674
55604	CARMIL1	HTA11_6818_2000001011	Human	Colorectum	AD	2.58e-06	-5.16e-01	0.0112
55604	CARMIL1	HTA11_6818_2000001021	Human	Colorectum	AD	2.14e-05	-5.03e-01	0.0588
55604	CARMIL1	HTA11_99999970781_79442	Human	Colorectum	MSS	1.01e-88	-1.27e+00	0.294
55604	CARMIL1	HTA11_99999965062_69753	Human	Colorectum	MSI-H	5.16e-05	-1.27e+00	0.3487

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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
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
Prostate		BPH: Benign Prostatic Hyperplasia
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:00514942	Colorectum	MSS	negative regulation of cytoskeleton organization	47/3467	163/18723	8.45e-04	8.71e-03	47
GO:00308342	Colorectum	MSS	regulation of actin filament depolymerization	20/3467	54/18723	1.04e-03	1.03e-02	20
GO:00510162	Colorectum	MSS	barbed-end actin filament capping	12/3467	26/18723	1.16e-03	1.12e-02	12
GO:00300321	Colorectum	MSS	lamellipodium assembly	24/3467	72/18723	1.91e-03	1.66e-02	24
GO:00310322	Colorectum	MSS	actomyosin structure organization	53/3467	196/18723	2.04e-03	1.75e-02	53
GO:00300382	Colorectum	MSS	contractile actin filament bundle assembly	32/3467	106/18723	2.41e-03	1.96e-02	32
GO:00431492	Colorectum	MSS	stress fiber assembly	32/3467	106/18723	2.41e-03	1.96e-02	32
GO:00516932	Colorectum	MSS	actin filament capping	15/3467	41/18723	4.88e-03	3.40e-02	15
GO:00308352	Colorectum	MSS	negative regulation of actin filament depolymerization	16/3467	45/18723	5.12e-03	3.51e-02	16
GO:01100202	Colorectum	MSS	regulation of actomyosin structure organization	29/3467	100/18723	6.99e-03	4.49e-02	29
GO:00322312	Colorectum	MSS	regulation of actin filament bundle assembly	30/3467	105/18723	7.74e-03	4.84e-02	30
GO:00322332	Colorectum	MSS	positive regulation of actin filament bundle assembly	20/3467	63/18723	8.06e-03	4.91e-02	20
GO:00226043	Colorectum	MSI-H	regulation of cell morphogenesis	45/1319	309/18723	2.70e-06	1.54e-04	45
GO:00432543	Colorectum	MSI-H	regulation of protein-containing complex assembly	56/1319	428/18723	5.25e-06	2.70e-04	56
GO:19000243	Colorectum	MSI-H	regulation of substrate adhesion-dependent cell spreading	15/1319	57/18723	6.36e-06	3.18e-04	15
GO:00313343	Colorectum	MSI-H	positive regulation of protein-containing complex assembly	36/1319	237/18723	1.02e-05	4.79e-04	36
GO:19000263	Colorectum	MSI-H	positive regulation of substrate adhesion-dependent cell spreading	12/1319	41/18723	1.65e-05	7.10e-04	12
GO:00329703	Colorectum	MSI-H	regulation of actin filament-based process	49/1319	397/18723	8.99e-05	2.90e-03	49
GO:00322733	Colorectum	MSI-H	positive regulation of protein polymerization	23/1319	138/18723	9.40e-05	2.98e-03	23
GO:00322713	Colorectum	MSI-H	regulation of protein polymerization	33/1319	233/18723	9.65e-05	3.03e-03	33

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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

CARMIL1

SNV

Missense_Mutation

novel

c.1550N>A

p.Gly517Asp

p.G517D

Q5VZK9

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A09Z-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CARMIL1

SNV

Missense_Mutation

c.3439G>T

p.Asp1147Tyr

p.D1147Y

Q5VZK9

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.987)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

CARMIL1

SNV

Missense_Mutation

c.1533N>G

p.Ile511Met

p.I511M

Q5VZK9

protein_coding

deleterious(0)

probably_damaging(0.999)

TCGA-D8-A1XK-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicine+cyclophosphamide

CARMIL1

SNV

Missense_Mutation

rs555687744

c.410N>A

p.Arg137His

p.R137H

Q5VZK9

protein_coding

deleterious(0.01)

probably_damaging(0.998)

TCGA-D8-A27W-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

doxorubicine+cyclophosphamide

CARMIL1

SNV

Missense_Mutation

c.1496N>T

p.Ser499Phe

p.S499F

Q5VZK9

protein_coding

tolerated(0.12)

probably_damaging(0.987)

TCGA-E2-A10C-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

CARMIL1

SNV

Missense_Mutation

novel

c.3268N>A

p.Glu1090Lys

p.E1090K

Q5VZK9

protein_coding

deleterious_low_confidence(0.03)

benign(0.092)

TCGA-E9-A22E-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphane

CARMIL1

SNV

Missense_Mutation

c.3269N>T

p.Glu1090Val

p.E1090V

Q5VZK9

protein_coding

deleterious_low_confidence(0.01)

benign(0.125)

TCGA-E9-A22E-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphane

CARMIL1

SNV

Missense_Mutation

c.3402N>T

p.Glu1134Asp

p.E1134D

Q5VZK9

protein_coding

tolerated_low_confidence(0.12)

benign(0.009)

TCGA-E9-A22E-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cyclophosphane

CARMIL1

SNV

Missense_Mutation

rs767321872

c.3466C>T

p.Arg1156Trp

p.R1156W

Q5VZK9

protein_coding

deleterious_low_confidence(0.03)

probably_damaging(0.969)

TCGA-GI-A2C8-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Unspecific

Adriamycin

CARMIL1

SNV

Missense_Mutation

novel

c.3489N>T

p.Met1163Ile

p.M1163I

Q5VZK9

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.958)

TCGA-LL-A5YN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

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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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