LSTrAP-Crowd: Prediction of novel components of bacterial ribosomes with crowd-sourced analysis of RNA sequencing data
Authors: Hew Benedict , Tan Qiao Wen , Goh William , Xiong Ng Jonathan Wei , Koh Kenny , Feng Rugdee Ryan Chieh , Teng Zheng Kai , Tan Jun Xiong , Yei Xi , Tan Qing Rong , Binte Sulaiman Ifa Syafiqah , Li Gilia Seo Min , Fajardo Villanueva Erielle Marie , Nguyen Son Thanh , Putri Dhira Anindya , Siying Jovi Tan , Ren Johanan Teo Yong , Tan Jia Wei , Ning Koh Shao , Gladys  , Ong Wei Wen , Moo Jia Rong , Koh Jace , Lim Pei Xuan , Teoh Shook Wei , Tamilselvam Pravin , Hui Harvard , Chua Yi Xuan , Ow Yeong Yook Kit , Hua Tay Jian , Chong Ming Jun , Sho Yu Wei , Xing Tang Bridget Jing , Kwantalalu Carissa Yuwono , Mohammad Rizal Nur Afiqah Binte , Tan Wei Heng , Chun Lim Shan , Tze Tan Sherianne Yen , Ying Tan Jia , Luminary Audrey Michelle , Jia Lim Jia , Jolyn  , Lunardi Vanessa , Low Ann Don , Abdul Rahim M K , Ming Lin , Ng Joseph JQ , Tsou Han , Jiayi Cheryl Lim , Hui Wen Teffarina Tay , Fang Wei Valerie Teo , Sheng Justin Tan You , Oktavina Shellia , Binte Roslan Aaminatul Khalishah , Chee Natasha Cassandra , Hui Xin Zoe Chen , Le Nguyen Nhi Uyen , Marta Tristy Abigayle , Jia’En Poh , Ying Ang Wei , Qi Ye Alena Tay , Yeow Emile Chiu Wei , Xanaz Wong , Rui Lee Xylon Wei , Wen Kelly Wong Pei , Tan Zhe Jun , R Vishalini Val , Yip Rayna , Chua Cherlyn , Boon Kai Lun , Mulupuri Sriya , Shan Lim Yuen , Suhui Samantha Chee , Wei Jin Amanda Crystal Lee , Tey Siew Choo , Neo Qi Ying , Hue Chan Yi , Xin Phua Tian , Sze Qi Ana Ho , Rodrigues Edbert E. , En Chan Mu , Sim Dynn , Chee Marcus , Ho Abigail , hui Ang Wen , Wong Bertrand , Zhao Margaret X , Ching Gabbie Er Kian , Grace Deng Zheyun , Tan Xin Yi , Foong Melissa , Rui Rachel Lim Qin , Lim Alyssa Jiaqi , Xuan Seow Jia , Reji Rinta P. , Menon Devika , Xuan Ong Xuan , Nicole  , Keerthana Ravi , Wong Min Jia , D’Rozario Zachary J , Lim Shing Yee , Lee Nicholas , Ni Ying , Lian Ying , Poh Jing Wen , Adrian Lee Ming Jern , Chandran Pravenah Ravi , Ngiaw Jia Xin , Foo Herman , Poon Joash , Chan Tong Ling , Ng Perry , Ng Ashlyn Xuanqi , Ong Zhen Ying , Xuan Trena Lee Wan , Min Kristy Lim Shi , Thng Yu Xuan , Yi Shirley Ong Si , Chu Sau Thi , Samantha Lim Shu Hua , Ho Jun Sheng , Phang Celest Lixuan , Le Yi Victoria Toh , Ng Peiran , Song Seetoh Wei , Shue Ern Manessa Nah , Mutwil Marek 
Published: April 2020

AbstractBacterial resistance to antibiotics is a growing problem that is projected to cause more deaths than cancer in 2050. Consequently, novel antibiotics are urgently needed. Since more than half of the available antibiotics target the bacterial ribosomes, proteins that are involved in protein synthesis are thus prime targets for the development of novel antibiotics. However, experimental identification of these potential antibiotic target proteins can be labor-intensive and challenging, as these proteins are likely to be poorly characterized and specific to few bacteria. In order to identify these novel proteins, we established a Large-Scale Transcriptomic Analysis Pipeline in Crowd (LSTrAP-Crowd), where 285 individuals processed 26 terabytes of RNA-sequencing data of the 17 most notorious bacterial pathogens. In total, the crowd processed 26,269 RNA-seq experiments and used the data to construct gene co-expression networks, which were used to identify more than a hundred uncharacterized genes that were transcriptionally associated with protein synthesis. We provide the identity of these genes together with the processed gene expression data. The data can be used to identify other vulnerabilities or bacteria, while our approach demonstrates how the processing of gene expression data can be easily crowdsourced.