Data collection and analysis

An easy-to-use pre-compiled data of the XENA platform were downloaded from UCSC (https://xenabrowser.net/datapages/). A total of 88 osteosarcoma cases expression matrix of GDC TARGET osteosarcoma project from the data were included in the present research. The expression matrix of the 58,387 genes, based on the log2(FPKM + 1), was collected in the GDC TARGET osteosarcoma project on July 23, 2019.

The clinical information was downloaded from the XENA platform provided by UCSC on September 13, 2018. Patients surviving less than 30 days were excluded from this study, overall survival data from 85 patient samples were included in the study. Using survival (3.2–10 version) and surviminer (0.4.9 version) packages, these overall survival-related genes were identified.

In addition, a microarray included 37 osteosarcoma cases, and related clinical information data were collected from the {"type":"entrez-geo","attrs":{"text":"GSE39055","term_id":"39055"}}GSE39055 of the open Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) database. Based on survival (3.2–10 version) and surviminer (0.4.9 version) packages, these overall survival-related genes were demonstrated. Based on the R software (3.6.3 version), the crucial overall-survival-related genes and lncRNAs were selected and visualized by ggplot2 package (3.3.3 version). To further identify the expression of lncRNAs between osteosarcoma and control samples, {"type":"entrez-geo","attrs":{"text":"GSE12865","term_id":"12865"}}GSE12865, which included 2 control osteoblast cell lines and 12 osteosarcoma cell lines, was downloaded from the GEO database (Additional file 1).

Tissues and clinical information of 62 patients (32 osteosarcoma, 12 lipomatous, 7 myomatous neoplasms, 6 nerve sheath tumors, and 5 synovial-like neoplasms) were provided by the Second Affiliated Hospital of Nanchang University from January 2012 to December 2016 as an external validation cohort. Survival distributions of clinical data were estimated using the log-rank test. Before collecting pathological tissue by puncture, no patient had received chemotherapy or radiotherapy. The metastatic status of the patients was evaluated at the first time of diagnosis. The clinical information of patients was shown in Table ​Table1.1. The present study was approved by the Ethics Committee of The Second Affiliated Hospital of Nanchang University [Review (2020) No. (115)]. Written informed consent was obtained from all participants. All tissue samples were preserved in liquid nitrogen until RNA extraction.

Baseline clinical characteristics of validation cohort