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: ADCY9

Gene summary for ADCY9

Gene summary.

Gene information	Species	Human
	Gene symbol	ADCY9
	Gene ID	115
	Gene name	adenylate cyclase 9
	Gene Alias	AC9
	Cytomap	16p13.3
	Gene Type	protein-coding
	GO ID	GO:0001701
	UniProtAcc	O60503

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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
115	ADCY9	HTA11_3410_2000001011	Human	Colorectum	AD	3.33e-09	-4.38e-01	0.0155
115	ADCY9	HTA11_866_3004761011	Human	Colorectum	AD	1.73e-04	-3.54e-01	0.096
115	ADCY9	HTA11_7696_3000711011	Human	Colorectum	AD	1.92e-06	-3.58e-01	0.0674
115	ADCY9	HTA11_99999970781_79442	Human	Colorectum	MSS	6.31e-15	-3.94e-01	0.294
115	ADCY9	HTA11_99999974143_84620	Human	Colorectum	MSS	3.15e-16	-5.07e-01	0.3005
115	ADCY9	F007	Human	Colorectum	FAP	2.51e-08	-4.68e-01	0.1176
115	ADCY9	A002-C-010	Human	Colorectum	FAP	3.10e-10	-4.01e-01	0.242
115	ADCY9	A001-C-207	Human	Colorectum	FAP	3.07e-10	-5.19e-01	0.1278
115	ADCY9	A015-C-203	Human	Colorectum	FAP	1.49e-27	-5.04e-01	-0.1294
115	ADCY9	A015-C-204	Human	Colorectum	FAP	4.11e-11	-4.39e-01	-0.0228
115	ADCY9	A014-C-040	Human	Colorectum	FAP	3.33e-04	-4.93e-01	-0.1184
115	ADCY9	A002-C-201	Human	Colorectum	FAP	2.89e-21	-5.59e-01	0.0324
115	ADCY9	A002-C-203	Human	Colorectum	FAP	4.39e-15	-4.83e-01	0.2786
115	ADCY9	A001-C-119	Human	Colorectum	FAP	1.19e-05	-2.78e-01	-0.1557
115	ADCY9	A001-C-108	Human	Colorectum	FAP	1.13e-23	-4.45e-01	-0.0272
115	ADCY9	A002-C-205	Human	Colorectum	FAP	2.38e-19	-4.52e-01	-0.1236
115	ADCY9	A001-C-104	Human	Colorectum	FAP	7.21e-09	-4.06e-01	0.0184
115	ADCY9	A015-C-005	Human	Colorectum	FAP	1.71e-04	-2.59e-01	-0.0336
115	ADCY9	A015-C-006	Human	Colorectum	FAP	1.15e-10	-3.91e-01	-0.0994
115	ADCY9	A015-C-106	Human	Colorectum	FAP	7.48e-15	-3.99e-01	-0.0511

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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
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:0009150	Colorectum	AD	purine ribonucleotide metabolic process	142/3918	368/18723	4.29e-15	1.17e-12	142
GO:0006163	Colorectum	AD	purine nucleotide metabolic process	149/3918	396/18723	1.08e-14	2.80e-12	149
GO:0072521	Colorectum	AD	purine-containing compound metabolic process	153/3918	416/18723	4.34e-14	1.01e-11	153
GO:0009259	Colorectum	AD	ribonucleotide metabolic process	144/3918	385/18723	5.25e-14	1.13e-11	144
GO:0019693	Colorectum	AD	ribose phosphate metabolic process	145/3918	396/18723	3.01e-13	5.71e-11	145
GO:0009117	Colorectum	AD	nucleotide metabolic process	168/3918	489/18723	2.20e-12	3.36e-10	168
GO:0006753	Colorectum	AD	nucleoside phosphate metabolic process	169/3918	497/18723	4.99e-12	6.98e-10	169
GO:0009152	Colorectum	AD	purine ribonucleotide biosynthetic process	64/3918	169/18723	3.09e-07	1.22e-05	64
GO:0009260	Colorectum	AD	ribonucleotide biosynthetic process	66/3918	182/18723	1.25e-06	4.02e-05	66
GO:0046390	Colorectum	AD	ribose phosphate biosynthetic process	67/3918	190/18723	3.21e-06	9.05e-05	67
GO:0006164	Colorectum	AD	purine nucleotide biosynthetic process	66/3918	191/18723	8.22e-06	1.97e-04	66
GO:0072522	Colorectum	AD	purine-containing compound biosynthetic process	68/3918	200/18723	1.12e-05	2.55e-04	68
GO:0001701	Colorectum	AD	in utero embryonic development	110/3918	367/18723	2.36e-05	4.62e-04	110
GO:1901293	Colorectum	AD	nucleoside phosphate biosynthetic process	80/3918	256/18723	6.31e-05	1.05e-03	80
GO:0009165	Colorectum	AD	nucleotide biosynthetic process	79/3918	254/18723	8.33e-05	1.30e-03	79
GO:00061632	Colorectum	MSS	purine nucleotide metabolic process	128/3467	396/18723	2.04e-11	3.02e-09	128
GO:00091502	Colorectum	MSS	purine ribonucleotide metabolic process	121/3467	368/18723	2.08e-11	3.02e-09	121
GO:00725212	Colorectum	MSS	purine-containing compound metabolic process	132/3467	416/18723	4.13e-11	4.86e-09	132
GO:00092592	Colorectum	MSS	ribonucleotide metabolic process	123/3467	385/18723	1.17e-10	1.20e-08	123
GO:00196932	Colorectum	MSS	ribose phosphate metabolic process	124/3467	396/18723	4.11e-10	3.49e-08	124

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa04714	Colorectum	AD	Thermogenesis	120/2092	232/8465	2.76e-19	1.16e-17	7.37e-18	120
hsa05110	Colorectum	AD	Vibrio cholerae infection	29/2092	50/8465	5.10e-07	7.12e-06	4.54e-06	29
hsa04723	Colorectum	AD	Retrograde endocannabinoid signaling	59/2092	148/8465	2.94e-05	2.73e-04	1.74e-04	59
hsa04213	Colorectum	AD	Longevity regulating pathway - multiple species	27/2092	62/8465	8.72e-04	5.96e-03	3.80e-03	27
hsa04015	Colorectum	AD	Rap1 signaling pathway	71/2092	210/8465	1.72e-03	9.68e-03	6.18e-03	71
hsa05163	Colorectum	AD	Human cytomegalovirus infection	75/2092	225/8465	2.00e-03	1.10e-02	7.01e-03	75
hsa04912	Colorectum	AD	GnRH signaling pathway	35/2092	93/8465	3.69e-03	1.90e-02	1.21e-02	35
hsa05166	Colorectum	AD	Human T-cell leukemia virus 1 infection	72/2092	222/8465	5.24e-03	2.44e-02	1.55e-02	72
hsa04962	Colorectum	AD	Vasopressin-regulated water reabsorption	19/2092	44/8465	5.48e-03	2.48e-02	1.58e-02	19
hsa04211	Colorectum	AD	Longevity regulating pathway	33/2092	89/8465	6.15e-03	2.68e-02	1.71e-02	33
hsa04971	Colorectum	AD	Gastric acid secretion	29/2092	76/8465	6.25e-03	2.68e-02	1.71e-02	29
hsa04928	Colorectum	AD	Parathyroid hormone synthesis, secretion and action	38/2092	106/8465	6.60e-03	2.77e-02	1.76e-02	38
hsa04972	Colorectum	AD	Pancreatic secretion	36/2092	102/8465	1.06e-02	3.98e-02	2.54e-02	36
hsa047141	Colorectum	AD	Thermogenesis	120/2092	232/8465	2.76e-19	1.16e-17	7.37e-18	120
hsa051101	Colorectum	AD	Vibrio cholerae infection	29/2092	50/8465	5.10e-07	7.12e-06	4.54e-06	29
hsa047231	Colorectum	AD	Retrograde endocannabinoid signaling	59/2092	148/8465	2.94e-05	2.73e-04	1.74e-04	59
hsa042131	Colorectum	AD	Longevity regulating pathway - multiple species	27/2092	62/8465	8.72e-04	5.96e-03	3.80e-03	27
hsa040151	Colorectum	AD	Rap1 signaling pathway	71/2092	210/8465	1.72e-03	9.68e-03	6.18e-03	71
hsa051631	Colorectum	AD	Human cytomegalovirus infection	75/2092	225/8465	2.00e-03	1.10e-02	7.01e-03	75
hsa049121	Colorectum	AD	GnRH signaling pathway	35/2092	93/8465	3.69e-03	1.90e-02	1.21e-02	35

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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

ADCY9

SNV

Missense_Mutation

c.3996N>A

p.Asp1332Glu

p.D1332E

O60503

protein_coding

deleterious_low_confidence(0.05)

benign(0.03)

TCGA-A7-A26H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Hormone Therapy

anastrozole

ADCY9

SNV

Missense_Mutation

rs149465612

c.3601G>A

p.Gly1201Ser

p.G1201S

O60503

protein_coding

deleterious(0)

probably_damaging(1)

TCGA-A8-A079-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Chemotherapy

5-fluorouracil

ADCY9

SNV

Missense_Mutation

c.1497C>G

p.Ile499Met

p.I499M

O60503

protein_coding

deleterious(0)

benign(0.186)

TCGA-A8-A07L-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

ADCY9

SNV

Missense_Mutation

c.4010N>A

p.Gly1337Glu

p.G1337E

O60503

protein_coding

tolerated_low_confidence(0.45)

benign(0.001)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ADCY9

SNV

Missense_Mutation

c.2831N>G

p.Ser944Cys

p.S944C

O60503

protein_coding

tolerated(0.27)

possibly_damaging(0.533)

TCGA-AC-A23H-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ADCY9

SNV

Missense_Mutation

rs772697228

c.1630G>A

p.Glu544Lys

p.E544K

O60503

protein_coding

tolerated(0.3)

benign(0.001)

TCGA-AN-A046-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

ADCY9

SNV

Missense_Mutation

c.1711N>T

p.Ile571Leu

p.I571L

O60503

protein_coding

deleterious(0.03)

benign(0.038)

TCGA-AN-A0AT-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ADCY9

SNV

Missense_Mutation

novel

c.2944N>A

p.Val982Met

p.V982M

O60503

protein_coding

deleterious(0.02)

benign(0.097)

TCGA-AN-A0FS-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

ADCY9

SNV

Missense_Mutation

c.2158N>C

p.Ile720Leu

p.I720L

O60503

protein_coding

tolerated(0.99)

benign(0.041)

TCGA-AO-A1KT-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Chemotherapy

fluorouracil

ADCY9

SNV

Missense_Mutation

c.2099N>T

p.Gly700Val

p.G700V

O60503

protein_coding

tolerated(0.12)

benign(0.24)

TCGA-AR-A0U3-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

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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
115	ADCY9	KINASE, ENZYME, DRUGGABLE GENOME		NSC-270718	CHEMBL401844	18630896
115	ADCY9	KINASE, ENZYME, DRUGGABLE GENOME		dalcetrapib	DALCETRAPIB	25583994

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