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: MED1

Gene summary for MED1

Gene summary.

Gene information	Species	Human
	Gene symbol	MED1
	Gene ID	5469
	Gene name	mediator complex subunit 1
	Gene Alias	CRSP1
	Cytomap	17q12
	Gene Type	protein-coding
	GO ID	GO:0000003
	UniProtAcc	Q15648

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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
5469	MED1	GSM4909291	Human	Breast	IDC	2.79e-50	1.04e+00	0.1753
5469	MED1	GSM4909292	Human	Breast	IDC	2.16e-03	4.18e-01	0.1236
5469	MED1	GSM4909293	Human	Breast	IDC	1.82e-56	8.34e-01	0.1581
5469	MED1	GSM4909317	Human	Breast	IDC	2.82e-02	1.51e-01	0.1355
5469	MED1	DCIS2	Human	Breast	DCIS	2.67e-20	8.42e-02	0.0085
5469	MED1	LZE2T	Human	Esophagus	ESCC	1.06e-02	2.93e-01	0.082
5469	MED1	LZE4T	Human	Esophagus	ESCC	3.44e-08	2.66e-01	0.0811
5469	MED1	LZE5T	Human	Esophagus	ESCC	3.23e-07	3.71e-01	0.0514
5469	MED1	LZE7T	Human	Esophagus	ESCC	1.35e-09	4.22e-01	0.0667
5469	MED1	LZE8T	Human	Esophagus	ESCC	1.06e-02	1.75e-01	0.067
5469	MED1	LZE22T	Human	Esophagus	ESCC	3.41e-03	1.82e-01	0.068
5469	MED1	LZE24T	Human	Esophagus	ESCC	3.13e-17	4.21e-01	0.0596
5469	MED1	LZE21T	Human	Esophagus	ESCC	8.40e-03	1.84e-01	0.0655
5469	MED1	P1T-E	Human	Esophagus	ESCC	2.31e-06	2.79e-01	0.0875
5469	MED1	P2T-E	Human	Esophagus	ESCC	1.92e-17	3.23e-01	0.1177
5469	MED1	P4T-E	Human	Esophagus	ESCC	2.12e-16	3.12e-01	0.1323
5469	MED1	P5T-E	Human	Esophagus	ESCC	9.36e-08	1.65e-01	0.1327
5469	MED1	P8T-E	Human	Esophagus	ESCC	9.37e-19	3.74e-01	0.0889
5469	MED1	P9T-E	Human	Esophagus	ESCC	1.82e-10	2.21e-01	0.1131
5469	MED1	P10T-E	Human	Esophagus	ESCC	7.15e-07	1.64e-01	0.116

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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
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

∗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:190495122	Liver	HCC	positive regulation of establishment of protein localization	207/7958	319/18723	3.95e-16	3.29e-14	207
GO:000688821	Liver	HCC	endoplasmic reticulum to Golgi vesicle-mediated transport	100/7958	130/18723	1.15e-15	8.67e-14	100
GO:001605021	Liver	HCC	vesicle organization	194/7958	300/18723	5.58e-15	3.97e-13	194
GO:000188922	Liver	HCC	liver development	108/7958	147/18723	2.16e-14	1.41e-12	108
GO:005122222	Liver	HCC	positive regulation of protein transport	194/7958	303/18723	2.41e-14	1.56e-12	194
GO:006100822	Liver	HCC	hepaticobiliary system development	109/7958	150/18723	5.72e-14	3.42e-12	109
GO:001703811	Liver	HCC	protein import	140/7958	206/18723	1.12e-13	6.46e-12	140
GO:003052222	Liver	HCC	intracellular receptor signaling pathway	171/7958	265/18723	3.00e-13	1.61e-11	171
GO:000690021	Liver	HCC	vesicle budding from membrane	53/7958	61/18723	7.38e-13	3.80e-11	53
GO:003166722	Liver	HCC	response to nutrient levels	276/7958	474/18723	2.30e-12	1.08e-10	276
GO:004854522	Liver	HCC	response to steroid hormone	206/7958	339/18723	6.81e-12	2.92e-10	206
GO:007149622	Liver	HCC	cellular response to external stimulus	191/7958	320/18723	3.40e-10	1.13e-08	191
GO:005165621	Liver	HCC	establishment of organelle localization	226/7958	390/18723	4.15e-10	1.34e-08	226
GO:00082022	Liver	HCC	steroid metabolic process	188/7958	319/18723	1.96e-09	5.63e-08	188
GO:007138322	Liver	HCC	cellular response to steroid hormone stimulus	128/7958	204/18723	3.92e-09	1.04e-07	128
GO:007180611	Liver	HCC	protein transmembrane transport	47/7958	59/18723	5.82e-09	1.51e-07	47
GO:000657521	Liver	HCC	cellular modified amino acid metabolic process	119/7958	188/18723	6.47e-09	1.67e-07	119
GO:003166812	Liver	HCC	cellular response to extracellular stimulus	149/7958	246/18723	7.35e-09	1.86e-07	149
GO:000758421	Liver	HCC	response to nutrient	111/7958	174/18723	1.10e-08	2.73e-07	111
GO:00901142	Liver	HCC	COPII-coated vesicle budding	27/7958	29/18723	1.28e-08	3.14e-07	27

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0491916	Breast	IDC	Thyroid hormone signaling pathway	23/867	121/8465	2.45e-03	1.69e-02	1.27e-02	23
hsa0491917	Breast	IDC	Thyroid hormone signaling pathway	23/867	121/8465	2.45e-03	1.69e-02	1.27e-02	23
hsa0491928	Esophagus	ESCC	Thyroid hormone signaling pathway	78/4205	121/8465	6.79e-04	2.23e-03	1.14e-03	78
hsa015227	Esophagus	ESCC	Endocrine resistance	63/4205	98/8465	2.38e-03	6.58e-03	3.37e-03	63
hsa04919113	Esophagus	ESCC	Thyroid hormone signaling pathway	78/4205	121/8465	6.79e-04	2.23e-03	1.14e-03	78
hsa0152215	Esophagus	ESCC	Endocrine resistance	63/4205	98/8465	2.38e-03	6.58e-03	3.37e-03	63
hsa0491912	Liver	HCC	Thyroid hormone signaling pathway	75/4020	121/8465	8.76e-04	3.38e-03	1.88e-03	75
hsa01522	Liver	HCC	Endocrine resistance	58/4020	98/8465	1.28e-02	3.19e-02	1.78e-02	58
hsa0491913	Liver	HCC	Thyroid hormone signaling pathway	75/4020	121/8465	8.76e-04	3.38e-03	1.88e-03	75
hsa015221	Liver	HCC	Endocrine resistance	58/4020	98/8465	1.28e-02	3.19e-02	1.78e-02	58
hsa015226	Oral cavity	OSCC	Endocrine resistance	63/3704	98/8465	3.09e-05	1.31e-04	6.67e-05	63
hsa0491926	Oral cavity	OSCC	Thyroid hormone signaling pathway	73/3704	121/8465	1.63e-04	5.52e-04	2.81e-04	73
hsa0152214	Oral cavity	OSCC	Endocrine resistance	63/3704	98/8465	3.09e-05	1.31e-04	6.67e-05	63
hsa04919112	Oral cavity	OSCC	Thyroid hormone signaling pathway	73/3704	121/8465	1.63e-04	5.52e-04	2.81e-04	73
hsa0152221	Prostate	Tumor	Endocrine resistance	37/1791	98/8465	1.17e-04	7.42e-04	4.60e-04	37
hsa0491925	Prostate	Tumor	Thyroid hormone signaling pathway	40/1791	121/8465	1.47e-03	6.26e-03	3.88e-03	40
hsa0152231	Prostate	Tumor	Endocrine resistance	37/1791	98/8465	1.17e-04	7.42e-04	4.60e-04	37
hsa0491934	Prostate	Tumor	Thyroid hormone signaling pathway	40/1791	121/8465	1.47e-03	6.26e-03	3.88e-03	40

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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

MED1

SNV

Missense_Mutation

novel

c.4150N>T

p.Val1384Leu

p.V1384L

Q15648

protein_coding

deleterious_low_confidence(0.04)

benign(0.01)

TCGA-AC-A3TM-01

Breast

breast invasive carcinoma

Female

<65

III/IV

Chemotherapy

cytoxan

MED1

SNV

Missense_Mutation

c.3950N>A

p.Ser1317Asn

p.S1317N

Q15648

protein_coding

deleterious_low_confidence(0.03)

benign(0.037)

TCGA-AN-A0FN-01

Breast

breast invasive carcinoma

Female

<65

I/II

Unknown

MED1

SNV

Missense_Mutation

c.3527N>T

p.Gly1176Val

p.G1176V

Q15648

protein_coding

tolerated_low_confidence(0.19)

possibly_damaging(0.609)

TCGA-AO-A0JM-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

doxorubicin

MED1

SNV

Missense_Mutation

novel

c.3094N>C

p.Thr1032Pro

p.T1032P

Q15648

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.996)

TCGA-B6-A1KF-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MED1

SNV

Missense_Mutation

rs764603504

c.2012N>A

p.Ser671Tyr

p.S671Y

Q15648

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.979)

TCGA-BH-A2L8-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

cytoxan

MED1

SNV

Missense_Mutation

c.2672N>G

p.Asp891Gly

p.D891G

Q15648

protein_coding

deleterious_low_confidence(0)

probably_damaging(0.94)

TCGA-D8-A1Y1-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

MED1

SNV

Missense_Mutation

c.440T>C

p.Phe147Ser

p.F147S

Q15648

protein_coding

deleterious(0)

probably_damaging(0.992)

TCGA-EW-A1OV-01

Breast

breast invasive carcinoma

Female

<65

I/II

Chemotherapy

epirubicin

MED1

insertion

In_Frame_Ins

novel

c.4587_4588insAAAAAATCTCATAGCATCAAG

p.Lys1523_Lys1529dup

p.K1523_K1529dup

Q15648

protein_coding

TCGA-A7-A0DB-01

Breast

breast invasive carcinoma

Female

<65

I/II

Hormone Therapy

arimidex

MED1

deletion

Frame_Shift_Del

c.1709delN

p.Gly570ValfsTer9

p.G570Vfs*9

Q15648

protein_coding

TCGA-AN-A0AK-01

Breast

breast invasive carcinoma

Female

>=65

I/II

Unknown

MED1

SNV

Missense_Mutation

rs199907019

c.1883N>T

p.Thr628Met

p.T628M

Q15648

protein_coding

deleterious_low_confidence(0)

benign(0.062)

TCGA-2W-A8YY-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

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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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