{"database":"GEO","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE256nnn/GSE256222/"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Transcriptomics"],"species":["Pseudomonas aeruginosa PAO1"],"gds_type":["Expression profiling by high throughput sequencing"],"full_dataset_link":["https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE256222"],"repository":["GEO"],"entry_type":["GSE"],"additional_accession":[]},"is_claimable":false,"name":"Characterization of Hypothetical Proteins Reveals Function Modules and Virulence Factors in Pseudomonas aeruginosa","description":"Uncharacterized hypothetical proteins (HPs) occupy 25-50 % of the bacterial genomes, known as dark matter, whose biological functions and regulatory processes remain mysterious. Pseudomonas aeruginosa is a superbug that causes a wide array of medical device-associated infection, and life-threatening acute or chronic infection in cystic fibrosis patient or immunocompromised individuals. In this study, we systematically revealed the functions of HPs using P. aeruginosa as a model strain. We constructed a HP deletion library that contains 938 deletion strains. Transcriptome profiling was performed to reveal a full picture of their differentially expressed genes (DEGs). We subsequently used independent component analysis (ICA) to cluster HPs into different modules with transcriptional regulatory network (TRN). The functions of 1087 HPs were determined by module and co-expression network. Combined with DEG-based virulence-associated network of HPs, we identified 33 novel virulence or antibiotic resistant-associated HPs using multiple methods and mice infection model, which are potential candidates to develop novel therapeutics against this superbug. We also revealed multiple groups of co-relationships between HPs and known virulence-associated transcription factors (TFs). In addition, we mapped the evolution of HPs in the Bacteria Kingdom, and highlighted a group of unique HPs with divergent functions in P. aeruginosa. Totally, this study annotated the functions of HPs in P. aeruginosa using transcriptome profiling coupled with machine learning, which provides an important HPs database for further studies on HPs in both eukaryotes and prokaryotes.","dates":{"publication":"2026/07/06"},"accession":"GSE256222","cross_references":{"GSM":["GSM8090088","GSM8090089","GSM8090091","GSM8090092","GSM8090093","GSM8090094","GSM8090095","GSM8090096","GSM8090097","GSM8090098","GSM8090090","GSM8090099","GSM8091397","GSM8090066","GSM8091398","GSM8090067","GSM8091399","GSM8090068","GSM8090069","GSM8090070","GSM8090071","GSM8090072","GSM8090073","GSM8090074","GSM8090075","GSM8090076","GSM8090077","GSM8090078","GSM8090079","GSM8090080","GSM8090081","GSM8090082","GSM8090083","GSM8090084","GSM8090085","GSM8090086","GSM8090087","GSM8091375","GSM8090044","GSM8091376","GSM8090045","GSM8090046","GSM8091377","GSM8090047","GSM8091378","GSM8091379","GSM8090048","GSM8090049","GSM8091380","GSM8091381","GSM8090050","GSM8091382","GSM8090051","GSM8090052","GSM8091383","GSM8091384","GSM8090053","GSM8091385","GSM8090054","GSM8090055","GSM8091386","GSM8090056","GSM8091387","GSM8091388","GSM8090057","GSM8091389","GSM8090058","GSM8090059","GSM8091390","GSM8091391","GSM8090060","GSM8091392","GSM8090061","GSM8090062","GSM8091393","GSM8091394","GSM8090063","GSM8090064","GSM8091395","GSM8090065","GSM8091396","GSM8091353","GSM8090022","GSM8091354","GSM8090023","GSM8091355","GSM8090024","GSM8091356","GSM8090025","GSM8091357","GSM8090026","GSM8090027","GSM8091358","GSM8090028","GSM8091359","GSM8090029","GSM8091360","GSM8091361","GSM8090030","GSM8091362","GSM8090031","GSM8091363","GSM8090032","GSM8091364","GSM8090033","GSM8091365","GSM8090034","GSM8091366","GSM8090035","GSM8091367","GSM8090036","GSM8090037","GSM8091368","GSM8090038","GSM8091369","GSM8090039","GSM8091370","GSM8091371","GSM8090040","GSM8091372","GSM8090041","GSM8091373","GSM8090042","GSM8091374","GSM8090043","GSM8090921","GSM8089932","GSM8089933","GSM8090922","GSM8090923","GSM8089930","GSM8090924","GSM8089931","GSM8090925","GSM8090926","GSM8090927","GSM8090928","GSM8090920","GSM8090929","GSM8089929","GSM8089927","GSM8089928","GSM8089925","GSM8089926","GSM8089923","GSM8089924","GSM8090932","GSM8089921","GSM8089922","GSM8090933","GSM8090934","GSM8090935","GSM8089920","GSM8090936","GSM8090937","GSM8090938","GSM8090939","GSM8090930","GSM8090931","GSM8089918","GSM8089919","GSM8089916","GSM8089917","GSM8089914","GSM8089915","GSM8089912","GSM8089913","GSM8089954","GSM8090900","GSM8089955","GSM8090901","GSM8089952","GSM8089953","GSM8090902","GSM8090903","GSM8089950","GSM8090904","GSM8089951","GSM8090905","GSM8090906","GSM8090907","GSM8090908","GSM8090909","GSM8089949","GSM8089947","GSM8089948","GSM8089945","GSM8089946","GSM8090910","GSM8089943","GSM8089944","GSM8090911","GSM8090912","GSM8089941","GSM8089942","GSM8090913","GSM8090914","GSM8090915","GSM8089940","GSM8090916","GSM8090917","GSM8090918","GSM8090919","GSM8089938","GSM8089939","GSM8089936","GSM8089937","GSM8089934","GSM8089935","GSM8089910","GSM8089911","GSM8089909","GSM8089907","GSM8089908","GSM8089905","GSM8089906","GSM8089903","GSM8089904","GSM8089901","GSM8089902","GSM8089900","GSM8090525","GSM8090526","GSM8090527","GSM8090528","GSM8090529","GSM8090520","GSM8090521","GSM8090522","GSM8090523","GSM8090524","GSM8090536","GSM8090537","GSM8090538","GSM8090539","GSM8090530","GSM8090531","GSM8090532","GSM8090533","GSM8090534","GSM8090535","GSM8090503","GSM8090987","GSM8089558","GSM8090988","GSM8089559","GSM8090504","GSM8089556","GSM8090505","GSM8090989","GSM8090506","GSM8089557","GSM8089554","GSM8090507","GSM8090508","GSM8089555","GSM8090509","GSM8089552","GSM8089553","GSM8090980","GSM8089551","GSM8090981","GSM8090982","GSM8090983","GSM8090984","GSM8090500","GSM8090501","GSM8090985","GSM8090986","GSM8090502","GSM8090514","GSM8090998","GSM8090515","GSM8090999","GSM8090516","GSM8090517","GSM8090518","GSM8090519","GSM8090990","GSM8090991","GSM8090992","GSM8090993","GSM8090994","GSM8090510","GSM8090511","GSM8090995","GSM8090512","GSM8090996","GSM8090513","GSM8090997","GSM8089976","GSM8090965","GSM8090966","GSM8089977","GSM8090967","GSM8089974","GSM8090968","GSM8089975","GSM8090969","GSM8089972","GSM8089973","GSM8089970","GSM8089971","GSM8090960","GSM8090961","GSM8090962","GSM8090963","GSM8090964","GSM8089969","GSM8089967","GSM8089968","GSM8089965","GSM8090976","GSM8090977","GSM8089966","GSM8090978","GSM8089963","GSM8089964","GSM8090979","GSM8089961","GSM8089962","GSM8089960","GSM8090970","GSM8090971","GSM8090972","GSM8090973","GSM8090974","GSM8090975","GSM8089958","GSM8089959","GSM8089956","GSM8089957","GSM8090943","GSM8089998","GSM8090944","GSM8089999","GSM8089996","GSM8090945","GSM8090946","GSM8089997","GSM8090947","GSM8089994","GSM8090948","GSM8089995","GSM8090949","GSM8089992","GSM8089993","GSM8089990","GSM8089991","GSM8090940","GSM8090941","GSM8090942","GSM8089989","GSM8089987","GSM8090954","GSM8089988","GSM8090955","GSM8089985","GSM8090956","GSM8090957","GSM8089986","GSM8090958","GSM8089983","GSM8089984","GSM8090959","GSM8089981","GSM8089982","GSM8089980","GSM8090950","GSM8090951","GSM8090952","GSM8090953","GSM8089978","GSM8089979","GSM8090129","GSM8090121","GSM809012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