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1. Data Source

All the gene expression datasets were collected from publicly available resources. The dataset id, resource, cancer types, primary sites, metastasis sites and the total number of samples for each dataset were listed below.

Dataset_ID	Resource	Cancer_Types	Primary_Sites	Metastasis_Sites	Sample_Number

TCGA-ACC	TCGA	adrenocortical carcinoma,kindey cancer	adrenal gland	bone,liver,lung,lymph node,other,peritoneal surfaces,soft tissue	79
TCGA-BLCA	TCGA	bladder cancer,bladder urothelial carcinoma	bladder	bone,liver,lung,lymph node,other	423
TCGA-BRCA	TCGA	breast cancer,breast invasive carcinoma	breast	bone,liver,lung,other	1188
TCGA-CESC	TCGA	cervical cancer,cervical squamous cell carcinoma and endocervical adenocarcinoma	cervix	head & neck,lung,other	309
TCGA-COAD	TCGA	colon adenocarcinoma,colorectal cancer	colorectal		453
TCGA-ESCA	TCGA	esophageal carcinoma,esophagus cancer	esophagus	bone,brain,liver,lung,other	171
GSE10893	GEO	breast cancer	breast	adrenal gland,brain,caudaequina,liver,lung,lymph node,skin,spinal cord	275
GSE11078	GEO	breast cancer	breast	lung,other	23
GSE12102	GEO	ewing's sarcoma	bone	unknown	37
GSE12276	GEO	breast cancer	breast	brain,breast,other	204
GSE12606	GEO	clear cell renal cell carcinoma,kindey cancer	kindey		6
GSE12630	GEO	breast cancer	breast	liver,lymph node,ovary	6
GSE14017	GEO	breast cancer	breast	bone,brain,lung	29
GSE14018	GEO	breast cancer	breast	bone,brain,liver,lung	36
GSE14020	GEO	breast cancer	breast	bone,brain,liver,lung	64
GSE14095	GEO	colorectal cancer	colorectum	liver	189
GSE14297	GEO	colorectal cancer	colorectum	liver	48
GSE14359	GEO	osteosarcoma	bone		12
GSE14378	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	lung	20
GSE14682	GEO	breast cancer	breast	brain	60
GSE14683	GEO	breast cancer	breast	brain	20
GSE15605	GEO	melanoma,skin cancer	skin	lymph node,other,subcutanious soft tissue,unknown	74
GSE1722	GEO	head and neck cancer,head and neck squamous cell carcinoma	hypopharynx,oropharynx		8
GSE18105	GEO	colorectal cancer	colorectum	unknown	111
GSE18462	GEO	colorectal cancer	colorectum	liver	8
GSE18549	GEO	breast cancer,colorectal cancer,lung cancer	breast,colorectum,lung	brain,chest wall,colorectum,liver,lung,lymph node	59
GSE19279	GEO	pancreatic cancer,pancreatic ductal adenocarcinoma	pancreas	liver	15
GSE19280	GEO	pancreatic cancer,pancreatic ductal adenocarcinoma	pancreas	liver	15
GSE1987	GEO	lung adenocarcinoma,lung cancer,lung squamous cell carcinoma	lung		32
GSE22153	GEO	melanoma,skin cancer	skin	lymph node,subcutaneous	56
GSE22541	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	adrenal gland,bone,liver,lung,lymph node,mediastinal,pancreas,parotis,renal,skin,soft tissue	61
GSE2280	GEO	oral cancer,oral squamous cell carcinoma	FOM,larynx,mandible,oral cavity,tongue	lymph node	27
GSE23629	GEO	kindey cancer,renal cell carcinoma	kindey	unknown	32
GSE26571	GEO	colorectal cancer	colorectum	liver,lymph node	24
GSE26964	GEO	prostate cancer	prostate	bone	13
GSE27162	GEO	midgut carcinoid tumor	midgut	liver,lymph node	39
GSE27635	GEO	hepatocellular carcinoma,liver cancer	liver	bone	96
GSE28248	GEO	hepatocellular carcinoma,liver cancer	liver	lymph node	80
GSE29827	GEO	lung adenocarcinoma,lung cancer,lung squamous cell carcinoma	lung	lymph node	5
GSE30480	GEO	breast cancer	breast	lymph node	20
GSE30587	GEO	ovarian cancer	ovary	omentum	18
GSE31232	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	chest wall	8
GSE31610	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	chest wall	9
GSE32269	GEO	castration resistant prostate cancer,prostate cancer	prostate	bone	33
GSE32489	GEO	breast cancer	breast	liver,lung,lymph node,spleen	104
GSE32906	GEO	nasopharynx cancer	nasopharynx	lymph node	22
GSE32981	GEO	osteosarcoma	costa,femur,fibula,humerus,pelvis,tibia	lung,lymph node,skeleton,soft tissue	18
GSE34153	GEO	pancreatic cancer	pancreas	fat,liver,lung,lymph node,muscle,pancreas	74
GSE3521	GEO	breast cancer	breast	adrenal gland,brain,caudaequina,liver,lung,lymph node,skin,spinal cord	170
GSE35834	GEO	colorectal cancer	colorectum	liver	80
GSE37407	GEO	breast cancer	breast	brain,liver,lymph node,ovary,skin	58
GSE38057	GEO	breast cancer	breast	brain	87
GSE3964	GEO	colorectal cancer	colorectum	liver	29
GSE40018	GEO	synovial sarcoma	synovium	unknown	34
GSE40367	GEO	cholangiocarcinoma,colon adenocarcinoma,colorectal cancer,hepatocellular carcinoma,liver cancer	colorectum,liver,stomach	adrenal gland,liver,lung,lymph node	54
GSE40911	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	bone,liver,lung	44
GSE40912	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	bone,liver,lung,peritoneum	32
GSE41874	GEO	hepatocellular carcinoma,liver cancer	liver	liver	9
GSE45114	GEO	hepatocellular carcinoma,liver cancer	liver	unknown	49
GSE46141	GEO	breast cancer	breast	bone,breast,liver,lung,lymph node,skin	90
GSE46563	GEO	breast cancer,lymph node negative breast cancer	breast	unknown	94
GSE46928	GEO	breast cancer	breast	brain	52
GSE47352	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	unknown	9
GSE49355	GEO	colorectal cancer	colorectum	liver	57
GSE50493	GEO	melanoma,skin cancer	skin	bone,brain,lung,lymph node,small intestine,soft tissue,spleen	68
GSE5327	GEO	ER negative breast cancer,breast cancer	breast	lung	58
GSE54088	GEO	colorectal cancer	colorectum	liver	34
GSE54323	GEO	breast cancer	breast	bone,liver,lymph node	14
GSE54492	GEO	melanoma,skin cancer	skin	lymph node,skin	25
GSE55198	GEO	seminoma,testicular cancer	testis	lymph node,unknown	8
GSE56350	GEO	colorectal cancer	colorectum	liver,lymph node	104
GSE56493	GEO	breast cancer	breast	bone,breast,liver,lymph node,skin	117
GSE57768	GEO	cutaneous squamous cell carcinoma,skin cancer	skin	unknown	47
GSE57780	GEO	papillary thyroid carcinoma,thyroid cancer	thyroid	lymph node	9
GSE58708	GEO	breast cancer	breast	liver,lymph node	8
GSE59745	GEO	prostate cancer	prostate	lymph node	41
GSE60464	GEO	melanoma,skin cancer	skin	lymph node,skin,soft tissue	42
GSE60542	GEO	papillary thyroid carcinoma,thyroid cancer	thyroid	lymph node,pleura	91
GSE61723	GEO	breast cancer,invasive ductal carcinomas,triple negative breast cancer	breast	lymph node	65
GSE62321	GEO	colorectal cancer	colorectum	liver	57
GSE62837	GEO	melanoma,skin cancer	skin	skin	5
GSE63119	GEO	colon adenocarcinoma,colorectal cancer	colorectum	unknown	49
GSE63124	GEO	pancreatic cancer	pancreas	liver,lung,peritoneum	16
GSE63668	GEO	brain cancer,medulloblastoma	brain	brain	22
GSE64256	GEO	colorectal cancer	colorectum	unknown	125
GSE65904	GEO	melanoma,skin cancer	skin	lymph node,skin,subcutaneous,viscera	195
GSE6605	GEO	prostate cancer	prostate	adrenal gland,liver,lymph node	66
GSE66271	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	unknown	26
GSE6752	GEO	prostate cancer	prostate	adrenal gland,liver,lymph node	19
GSE68468	GEO	colorectal cancer	colorectum	liver,lung	325
GSE70289	GEO	laryngeal cancer,laryngeal squamous cell carcinoma	larynx	unknown	15
GSE70534	GEO	small bowel neuroendocrine tumor,small intestine cancer	small intestine	liver,lymph node	87
GSE70574	GEO	colorectal cancer	colorectum	lymph node	16
GSE71222	GEO	colorectal cancer	colorectum	unknown	152
GSE72199	GEO	colorectal cancer	colorectum	liver	36
GSE72304	GEO	clear cell renal cell carcinoma,kindey cancer	kindey	chest wall	8
GSE73178	GEO	colorectal cancer	colorectum	liver	8
GSE73338	GEO	insulinoma,non-functional PanNET,pancreatic neuroendocrine tumor	pancreas	liver,lymph node	94
GSE73383	GEO	breast cancer,ductal breast adenocarcinoma	breast	unknown	38
GSE73652	GEO	eye cancer,uveal melanoma	eye	unknown	13
GSE7410	GEO	cervical cancer	cervix	lymph node	44
GSE74367	GEO	castration resistant prostate cancer,prostate cancer	prostate	bone,kindey,liver,lung,lymph node,peritoneum,posterior peritoneum	44
GSE74685	GEO	castration resistant prostate cancer,prostate cancer	prostate	adrenal gland,bone,kindey,liver,lung,lymph node,peritoneum,posterior peritoneum	145
GSE75117	GEO	colorectal cancer	colorectum	liver,ovary,peritoneum	37
GSE7553	GEO	basal cell skin cancer,melanoma,skin cancer,squamous cell carcinoma	skin	unknown	86
GSE76124	GEO	breast cancer,infiltrating ductal carcinoma	breast	unknown	141
GSE76714	GEO	breast cancer,triple negative breast cancer	breast	brain,other	71
GSE77199	GEO	colorectal cancer,kindey cancer,renal cell carcinoma	colorectum,kindey	liver	24
GSE80038	GEO	breast cancer,triple negative breast cancer	breast	lung	20
GSE84976	GEO	eye cancer,uveal melanoma	eye	unknown	28
GSE85258	GEO	clear cell renal cell carcinoma,kindey cancer,papillary renal cell carcinoma	kindey	lung	31
GSE85730	GEO	penile squamous cell carcinoma,penis cancer	penis	viscera	33
GSE87211	GEO	colorectal cancer	colorectum	unknown	361
GSE9348	GEO	colorectal cancer	colorectum	unknown	70
GSE9349	GEO	head and neck cancer,head and neck squamous cell carcinoma	larynx,mouth,oropharynx	unknown	22
GSE9893	GEO	breast cancer	breast	unknown	155
TCGA-PAAD	TCGA	pancreatic adenocarcinoma,pancreatic cancer	pancreas	liver,lung,peritoneal surfaces	173
TCGA-PRAD	TCGA	prostate adenocarcinoma,prostate cancer	prostate	bone,non-regional / distant lymph nodes,unknown	546
TCGA-STAD	TCGA	gastric cancer,stomach adenocarcinoma	stomach	liver,lung,non-regional / distant lymph nodes,other,peritoneal surfaces	404
TCGA-TGCT	TCGA	testicular cancer,testicular germ cell tumors	testis	liver,lung,lymph node	134
TCGA-THCA	TCGA	thyroid cancer,thyroid carcinoma	thyroid	bone,lung,other	567
TCGA-THYM	TCGA	thymoma	thymus	bone,brain,liver,other,pleura/pleural effusion	121
TCGA-UCEC	TCGA	cervical cancer,uterine corpus endometrial carcinoma	uterus	liver,other	559
TCGA-UCS	TCGA	cervical cancer,uterine carcinosarcoma	uterus	bone,brain,liver,lung,lymph node,other,pelvis	56
TCGA-UVM	TCGA	eye cancer,uveal melanoma	eye	liver,skin	80

2.The framework of the database construction in HCMDB

Data collection workflow

All the mRNA, miRNA and lncRNA expression datasets of metastasis were collected from NCBI Gene Expression Omnibus and TCGA datasets. Metastasis-related genes were manually curated from more than 7000 published literatures.

3. Gene search

You can search genes of your interest including protein-coding genes, lncRNAs and microRNAs by entering gene symbols or other gene ids (gene alias, gene old symbol, uniprot id, refseq acc, ensemble id, miRBase acc and so on). You can search genes in the home page and search page. Quick search allows single gene searching and bulk search allow 15 genes at most.

By clicking the ‘Submit’ button, you’ll see the search result, including summary, previous study about metastasis and expression analysis for each target.

4. Search results

5. Database browse

You can browse all experiments and filter interested results based on conditions about cancer type, primary site, metastatic site and gene type.

6. Experiment Details

DE mRNA，DE lncRNA and DE miRNA shows the differential expression analysis result, DEG function show GO and KEGG enrichment analysis result, DEG network shows the co-expression network of mRNA-mRNA and mRNA-lncRNA, the regulation network of miRNA-mRNA, miRNA-lncRNA and miRNA-mRNA-lncRNA.

example: mRNA-lncRNA coexpression network

example: miRNA-mRNA-lncRNA coexpression network