Step-by-step Guide to HCMDB

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-ACCTCGAadrenocortical carcinoma,kindey canceradrenal glandbone,liver,lung,lymph node,other,peritoneal surfaces,soft tissue79
TCGA-BLCATCGAbladder cancer,bladder urothelial carcinomabladderbone,liver,lung,lymph node,other423
TCGA-BRCATCGAbreast cancer,breast invasive carcinomabreastbone,liver,lung,other1188
TCGA-CESCTCGAcervical cancer,cervical squamous cell carcinoma and endocervical adenocarcinomacervixhead & neck,lung,other309
TCGA-COADTCGAcolon adenocarcinoma,colorectal cancercolorectal453
TCGA-ESCATCGAesophageal carcinoma,esophagus canceresophagusbone,brain,liver,lung,other171
GSE10893GEObreast cancerbreastadrenal gland,brain,caudaequina,liver,lung,lymph node,skin,spinal cord275
GSE11078GEObreast cancerbreastlung,other23
GSE12102GEOewing's sarcomaboneunknown37
GSE12276GEObreast cancerbreastbrain,breast,other204
GSE12606GEOclear cell renal cell carcinoma,kindey cancerkindey6
GSE12630GEObreast cancerbreastliver,lymph node,ovary6
GSE14017GEObreast cancerbreastbone,brain,lung29
GSE14018GEObreast cancerbreastbone,brain,liver,lung36
GSE14020GEObreast cancerbreastbone,brain,liver,lung64
GSE14095GEOcolorectal cancercolorectumliver189
GSE14297GEOcolorectal cancercolorectumliver48
GSE14359GEOosteosarcomabone12
GSE14378GEOclear cell renal cell carcinoma,kindey cancerkindeylung20
GSE14682GEObreast cancerbreastbrain60
GSE14683GEObreast cancerbreastbrain20
GSE15605GEOmelanoma,skin cancerskinlymph node,other,subcutanious soft tissue,unknown74
GSE1722GEOhead and neck cancer,head and neck squamous cell carcinomahypopharynx,oropharynx8
GSE18105GEOcolorectal cancercolorectumunknown111
GSE18462GEOcolorectal cancercolorectumliver8
GSE18549GEObreast cancer,colorectal cancer,lung cancerbreast,colorectum,lungbrain,chest wall,colorectum,liver,lung,lymph node59
GSE19279GEOpancreatic cancer,pancreatic ductal adenocarcinomapancreasliver15
GSE19280GEOpancreatic cancer,pancreatic ductal adenocarcinomapancreasliver15
GSE1987GEOlung adenocarcinoma,lung cancer,lung squamous cell carcinomalung32
GSE22153GEOmelanoma,skin cancerskinlymph node,subcutaneous56
GSE22541GEOclear cell renal cell carcinoma,kindey cancerkindeyadrenal gland,bone,liver,lung,lymph node,mediastinal,pancreas,parotis,renal,skin,soft tissue61
GSE2280GEOoral cancer,oral squamous cell carcinomaFOM,larynx,mandible,oral cavity,tonguelymph node27
GSE23629GEOkindey cancer,renal cell carcinomakindeyunknown32
GSE26571GEOcolorectal cancercolorectumliver,lymph node24
GSE26964GEOprostate cancerprostatebone13
GSE27162GEOmidgut carcinoid tumormidgutliver,lymph node39
GSE27635GEOhepatocellular carcinoma,liver cancerliverbone96
GSE28248GEOhepatocellular carcinoma,liver cancerliverlymph node80
GSE29827GEOlung adenocarcinoma,lung cancer,lung squamous cell carcinomalunglymph node5
GSE30480GEObreast cancerbreastlymph node20
GSE30587GEOovarian cancerovaryomentum18
GSE31232GEOclear cell renal cell carcinoma,kindey cancerkindeychest wall8
GSE31610GEOclear cell renal cell carcinoma,kindey cancerkindeychest wall9
GSE32269GEOcastration resistant prostate cancer,prostate cancerprostatebone33
GSE32489GEObreast cancerbreastliver,lung,lymph node,spleen104
GSE32906GEOnasopharynx cancernasopharynxlymph node22
GSE32981GEOosteosarcomacosta,femur,fibula,humerus,pelvis,tibialung,lymph node,skeleton,soft tissue18
GSE34153GEOpancreatic cancerpancreasfat,liver,lung,lymph node,muscle,pancreas74
GSE3521GEObreast cancerbreastadrenal gland,brain,caudaequina,liver,lung,lymph node,skin,spinal cord170
GSE35834GEOcolorectal cancercolorectumliver80
GSE37407GEObreast cancerbreastbrain,liver,lymph node,ovary,skin58
GSE38057GEObreast cancerbreastbrain87
GSE3964GEOcolorectal cancercolorectumliver29
GSE40018GEOsynovial sarcomasynoviumunknown34
GSE40367GEOcholangiocarcinoma,colon adenocarcinoma,colorectal cancer,hepatocellular carcinoma,liver cancercolorectum,liver,stomachadrenal gland,liver,lung,lymph node54
GSE40911GEOclear cell renal cell carcinoma,kindey cancerkindeybone,liver,lung44
GSE40912GEOclear cell renal cell carcinoma,kindey cancerkindeybone,liver,lung,peritoneum32
GSE41874GEOhepatocellular carcinoma,liver cancerliverliver9
GSE45114GEOhepatocellular carcinoma,liver cancerliverunknown49
GSE46141GEObreast cancerbreastbone,breast,liver,lung,lymph node,skin90
GSE46563GEObreast cancer,lymph node negative breast cancerbreastunknown94
GSE46928GEObreast cancerbreastbrain52
GSE47352GEOclear cell renal cell carcinoma,kindey cancerkindeyunknown9
GSE49355GEOcolorectal cancercolorectumliver57
GSE50493GEOmelanoma,skin cancerskinbone,brain,lung,lymph node,small intestine,soft tissue,spleen68
GSE5327GEOER negative breast cancer,breast cancerbreastlung58
GSE54088GEOcolorectal cancercolorectumliver34
GSE54323GEObreast cancerbreastbone,liver,lymph node14
GSE54492GEOmelanoma,skin cancerskinlymph node,skin25
GSE55198GEOseminoma,testicular cancertestislymph node,unknown8
GSE56350GEOcolorectal cancercolorectumliver,lymph node104
GSE56493GEObreast cancerbreastbone,breast,liver,lymph node,skin117
GSE57768GEOcutaneous squamous cell carcinoma,skin cancerskinunknown47
GSE57780GEOpapillary thyroid carcinoma,thyroid cancerthyroidlymph node9
GSE58708GEObreast cancerbreastliver,lymph node8
GSE59745GEOprostate cancerprostatelymph node41
GSE60464GEOmelanoma,skin cancerskinlymph node,skin,soft tissue42
GSE60542GEOpapillary thyroid carcinoma,thyroid cancerthyroidlymph node,pleura91
GSE61723GEObreast cancer,invasive ductal carcinomas,triple negative breast cancerbreastlymph node65
GSE62321GEOcolorectal cancercolorectumliver57
GSE62837GEOmelanoma,skin cancerskinskin5
GSE63119GEOcolon adenocarcinoma,colorectal cancercolorectumunknown49
GSE63124GEOpancreatic cancerpancreasliver,lung,peritoneum16
GSE63668GEObrain cancer,medulloblastomabrainbrain22
GSE64256GEOcolorectal cancercolorectumunknown125
GSE65904GEOmelanoma,skin cancerskinlymph node,skin,subcutaneous,viscera195
GSE6605GEOprostate cancerprostateadrenal gland,liver,lymph node66
GSE66271GEOclear cell renal cell carcinoma,kindey cancerkindeyunknown26
GSE6752GEOprostate cancerprostateadrenal gland,liver,lymph node19
GSE68468GEOcolorectal cancercolorectumliver,lung325
GSE70289GEOlaryngeal cancer,laryngeal squamous cell carcinomalarynxunknown15
GSE70534GEOsmall bowel neuroendocrine tumor,small intestine cancersmall intestineliver,lymph node87
GSE70574GEOcolorectal cancercolorectumlymph node16
GSE71222GEOcolorectal cancercolorectumunknown152
GSE72199GEOcolorectal cancercolorectumliver36
GSE72304GEOclear cell renal cell carcinoma,kindey cancerkindeychest wall8
GSE73178GEOcolorectal cancercolorectumliver8
GSE73338GEOinsulinoma,non-functional PanNET,pancreatic neuroendocrine tumorpancreasliver,lymph node94
GSE73383GEObreast cancer,ductal breast adenocarcinomabreastunknown38
GSE73652GEOeye cancer,uveal melanomaeyeunknown13
GSE7410GEOcervical cancercervixlymph node44
GSE74367GEOcastration resistant prostate cancer,prostate cancerprostatebone,kindey,liver,lung,lymph node,peritoneum,posterior peritoneum44
GSE74685GEOcastration resistant prostate cancer,prostate cancerprostateadrenal gland,bone,kindey,liver,lung,lymph node,peritoneum,posterior peritoneum145
GSE75117GEOcolorectal cancercolorectumliver,ovary,peritoneum37
GSE7553GEObasal cell skin cancer,melanoma,skin cancer,squamous cell carcinomaskinunknown86
GSE76124GEObreast cancer,infiltrating ductal carcinomabreastunknown141
GSE76714GEObreast cancer,triple negative breast cancerbreastbrain,other71
GSE77199GEOcolorectal cancer,kindey cancer,renal cell carcinomacolorectum,kindeyliver24
GSE80038GEObreast cancer,triple negative breast cancerbreastlung20
GSE84976GEOeye cancer,uveal melanomaeyeunknown28
GSE85258GEOclear cell renal cell carcinoma,kindey cancer,papillary renal cell carcinomakindeylung31
GSE85730GEOpenile squamous cell carcinoma,penis cancerpenisviscera33
GSE87211GEOcolorectal cancercolorectumunknown361
GSE9348GEOcolorectal cancercolorectumunknown70
GSE9349GEOhead and neck cancer,head and neck squamous cell carcinomalarynx,mouth,oropharynxunknown22
GSE9893GEObreast cancerbreastunknown155
TCGA-PAADTCGApancreatic adenocarcinoma,pancreatic cancerpancreasliver,lung,peritoneal surfaces173
TCGA-PRADTCGAprostate adenocarcinoma,prostate cancerprostatebone,non-regional / distant lymph nodes,unknown546
TCGA-STADTCGAgastric cancer,stomach adenocarcinomastomachliver,lung,non-regional / distant lymph nodes,other,peritoneal surfaces404
TCGA-TGCTTCGAtesticular cancer,testicular germ cell tumorstestisliver,lung,lymph node134
TCGA-THCATCGAthyroid cancer,thyroid carcinomathyroidbone,lung,other567
TCGA-THYMTCGAthymomathymusbone,brain,liver,other,pleura/pleural effusion121
TCGA-UCECTCGAcervical cancer,uterine corpus endometrial carcinomauterusliver,other559
TCGA-UCSTCGAcervical cancer,uterine carcinosarcomauterusbone,brain,liver,lung,lymph node,other,pelvis56
TCGA-UVMTCGAeye cancer,uveal melanomaeyeliver,skin80

2.The framework of the database construction in HCMDB

Data collection workflow

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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.

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

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4. Search results

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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.

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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.

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example: mRNA-lncRNA coexpression network

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example: miRNA-mRNA-lncRNA coexpression network

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