Data Collection and Curation

The selected peptides were translated from ncRNAs containing smORFs and were included in the database as per the same criteria as in the first version of FuncPEP: 1) validated by molecular biology techniques (MS, western blotting, immunohistochemistry, immunofluorescence) and/or indirect methods such as ribosome profiling and loss/gain of function studies by wet-lab experiments; 2) functionally characterized by demonstrating their involvement in physiological homeostasis or disease; and 3) size less than 100 aa in length. Some of the ncPEPs are validated only by indirect methods and are marked with an asterisk in the database and require further validation. NcPEPs identified by computational methods only were not included in the database. We used the same inclusion criteria as in the first version of FuncPEP, incorporating PubMed and Google Scholar search engines to identify and characterize ncPEPs in the database from 2020 to the present using the keyword (“functional peptides”, “antisense RNA,” OR “lincRNA”, OR “lncRNA”, OR “miRNA”, OR “circRNA”, OR “rRNA”, OR “tRNA”, OR “ncPEP”). Furthermore, one of the following terms were filtered incorporating translation (smORF,” OR “Ribo-seq”, OR “ribosome profiling”, OR “mass spectrometry”, OR “translation”).”

PubMed search incorporating the keywords was performed and screened for validated functional peptides derived from non-coding RNAs. The novel identified ncPEPs included in our database were characterized by a wide array of molecular and physiological parameters (i.e., types of host ncRNA, species distribution, chromosomal density, distribution of ncRNA length, identification methods, molecular weight and functional distribution across humans and other species). Exclusive to our database, we only included ncPEPs that were detected by direct means (MS, Western blotting, immunohistochemistry, immunofluorescence) or indirect means ((ribosome profiling, loss/gain of function studies) of experimental confirmation. All of our ncPEPs in the database are also functionally characterized which as well are linked with physiological and pathological processes.

A total of 15,805 articles were identified for the period August 2020 to July 2023. After accounting for duplicate articles, 10,502 articles were initially screened by title and abstract. Subsequently, 927 articles were selected for full-text evaluation to identify a wide range of biological and molecular features (i.e., species-specificity, type of RNA source, amino acid length, etc.) which are easily accessible through FuncPEP’s user-friendly interface. Of these 927 candidate studies, only 40 studies with a total of 40 validated functional ncPEPs, were included in the FuncPEP v2.0 database according to the stated inclusion criteria (Figure 1A). The updated version of the website, highlighted in this manuscript, includes the most recently investigated and characterized FuncPEPs to date (Figure 1B). Moreover, it was noted that not a large increase in the number of ncPEPs were identified in the last 3 years (Figure 1B). Throughout the last decade, the number of identified functional peptides has increased due to advances of standardized techniques. FuncPEP is designed to have a better user-friendly interface allowing researchers to have access to all validated ncPEPs discovered so far through a website. The website can be accessed via the following link (https://bioinformatics.mdanderson.org/Supplements/FuncPEP/). The major sections of the website are divided into (1) the Home section, which includes a description of the funcPEP, (2) the Database section, which includes a dynamic hyperlinked table browser providing detailed information about all ncPEPs, (3) Method section, which includes a description of the workflow that we used to collect and curate the ncPEPs characteristics, and (4) Help section, which includes details and aids the user on website navigation.

Distribution of ncPEP functions

Distribution of Human ncPEP functions

For inclusion of new ncPEPs please contact Dr. George Calin.

If you notice an error in the information provided by FuncPEP, do not hesitate to contact us.