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
