Abstract:
BACKGROUND:The recently developed RNA interference (RNAi) technology has created an unprecedented opportunity which allows the function of individual genes in whole organisms or cell lines to be interrogated at genome-wide scale. However, multiple issues, such as off-target effects or low efficacies in knocking down certain genes, have produced RNAi screening results that are often noisy and that potentially yield both high rates of false positives and false negatives. Therefore, integrating RNAi screening results with other information, such as protein-protein interaction (PPI), may help to address these issues. RESULTS:By analyzing 24 genome-wide RNAi screens interrogating various biological processes in Drosophila, we found that RNAi positive hits were significantly more connected to each other when analyzed within a protein-protein interaction network, as opposed to random cases, for nearly all screens. Based on this finding, we developed a network-based approach to identify false positives (FPs) and false negatives (FNs) in these screening results. This approach relied on a scoring function, which we termed NePhe, to integrate information obtained from both PPI network and RNAi screening results. Using a novel rank-based test, we compared the performance of different NePhe scoring functions and found that diffusion kernel-based methods generally outperformed others, such as direct neighbor-based methods. Using two genome-wide RNAi screens as examples, we validated our approach extensively from multiple aspects. We prioritized hits in the original screens that were more likely to be reproduced by the validation screen and recovered potential FNs whose involvements in the biological process were suggested by previous knowledge and mutant phenotypes. Finally, we demonstrated that the NePhe scoring system helped to biologically interpret RNAi results at the module level. CONCLUSION:By comprehensively analyzing multiple genome-wide RNAi screens, we conclude that network information can be effectively integrated with RNAi results to produce suggestive FPs and FNs, and to bring biological insight to the screening results.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Wang L,Tu Z,Sun Fdoi
10.1186/1471-2164-10-220subject
Has Abstractpub_date
2009-05-12 00:00:00pages
220issn
1471-2164pii
1471-2164-10-220journal_volume
10pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyse...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1004
更新日期:2014-11-20 00:00:00
abstract:BACKGROUND:Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-857
更新日期:2013-12-05 00:00:00
abstract:BACKGROUND:miRNAs are small, non-coding RNA molecules that mainly act as negative regulators of target gene messages. Due to their regulatory functions, they have lately been implicated in several diseases, including malignancies. Roughly half of known miRNA genes are located within previously annotated protein-coding ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-533
更新日期:2010-10-01 00:00:00
abstract:BACKGROUND:The importance of poultry as a global source of protein underpins the chicken genome and associated SNP data as key tools in selecting and breeding healthy robust birds with improved disease resistance. SNPs affecting host peptides involved in the innate defences tend to be rare, but three non-synonymous SNP...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4034-6
更新日期:2017-08-18 00:00:00
abstract:BACKGROUND:Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by chromatin immunoprecipitation sequencing (ChIP-Seq), protein-RNA interactions by crosslinking immun...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5362-x
更新日期:2019-01-05 00:00:00
abstract:BACKGROUND:Meiotic recombination is a fundamental evolutionary process. It not only generates diversity, but influences the efficacy of natural selection and genome evolution. There can be significant heterogeneity in recombination rates within and between species, however this variation is not well understood outside ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2884-y
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:The cellular proteome and metabolome are underlying dynamic regulation allowing rapid adaptation to changes in the environment. System-wide analysis of these dynamics will provide novel insights into mechanisms of stress adaptation for higher photosynthetic organisms. We applied pulsed-SILAC labeling to a ph...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-215
更新日期:2012-05-31 00:00:00
abstract:BACKGROUND:Grass carp (Ctenopharyngodon idella) belongs to the family Cyprinidae which includes more than 2000 fish species. It is one of the most important freshwater food fish species in world aquaculture. A linkage map is an essential framework for mapping traits of interest and is often the first step towards under...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-135
更新日期:2010-02-24 00:00:00
abstract:BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-448
更新日期:2013-07-05 00:00:00
abstract:BACKGROUND:Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-694
更新日期:2012-12-11 00:00:00
abstract:BACKGROUND:The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists exe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S6-S2
更新日期:2013-10-25 00:00:00
abstract:BACKGROUND:The pathogenesis-related (PR) group of proteins are operationally defined as polypeptides that increase in concentration in plant tissues upon contact with a pathogen. To date, 17 classes of highly divergent proteins have been described that act through multiple mechanisms of pathogen resistance. Characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2693-3
更新日期:2016-05-17 00:00:00
abstract:BACKGROUND:Nucleosomes facilitate the packaging of the eukaryotic genome and modulate the access of regulators to DNA. A detailed description of the nucleosomal organization under different transcriptional programmes is essential to understand their contribution to genomic regulation. RESULTS:To visualize the dynamics...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-813
更新日期:2013-11-21 00:00:00
abstract:BACKGROUND:Acinetobacter baumannii is a significant hospital pathogen, particularly due to the dissemination of highly multidrug resistant isolates. Genome data have revealed that A. baumannii is highly genetically diverse, which correlates with major variations seen at the phenotypic level. Thus far, comparative genom...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1020
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms). There are few studies that investi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-23
更新日期:2008-01-18 00:00:00
abstract:BACKGROUND:Nicotiana benthamiana is a widely used model plant species for research on plant-pathogen interactions as well as other areas of plant science. It can be easily transformed or agroinfiltrated, therefore it is commonly used in studies requiring protein localization, interaction, or plant-based systems for pro...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2209-6
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:The tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-726
更新日期:2010-12-24 00:00:00
abstract:BACKGROUND:Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator-prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, ty...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5647-8
更新日期:2019-05-09 00:00:00
abstract:BACKGROUND:Aneuploidies are copy number variants that affect entire chromosomes. They are seen commonly in cancer, embryonic stem cells, human embryos, and in various trisomic diseases. Aneuploidies frequently affect only a subset of cells in a sample; this is known as "mosaic" aneuploidy. A cell that harbours an aneup...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4253-x
更新日期:2017-11-25 00:00:00
abstract:BACKGROUND:Various cancer cells, including those of colorectal cancer (CRC), release microvesicles (exosomes) into surrounding tissues and peripheral circulation. These microvesicles can mediate communication between cells and affect various tumor-related processes in their target cells. RESULTS:We present potential r...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-556
更新日期:2009-11-25 00:00:00
abstract::ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-018-4614-0
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Candida albicans is a diploid pathogenic fungus not yet amenable to routine genetic investigations. Understanding aspects of the regulation of its biological functions and the assembly of its protein complexes would lead to further insight into the biology of this common disease-causing microbial agent. RES...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-578
更新日期:2008-12-02 00:00:00
abstract:BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5453-3
更新日期:2019-01-24 00:00:00
abstract:BACKGROUND:Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. RESULTS:Comparative analysis showed that the structure and evolutionary patterns of the I...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-743
更新日期:2014-08-30 00:00:00
abstract:BACKGROUND:Adult neurogenesis, which is the continual production of new neurons in the mature brain, demonstrates the strikingly plastic nature of the nervous system. Adult neural stem cells and their neural precursors, collectively referred to as neural progenitor cells (NPCs), are present in the subgranular zone (SGZ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-206
更新日期:2014-03-19 00:00:00
abstract:BACKGROUND:Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not suff...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4787-6
更新日期:2018-06-05 00:00:00
abstract:BACKGROUND:Lung aging is characterized by a number of structural alterations including fibrosis, chronic inflammation and the alteration of inflammatory cell composition. Chronic exposure to cigarette smoke (CS) is known to induce similar alterations and may contribute to premature lung aging. Additionally, aging and C...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6712-z
更新日期:2020-04-09 00:00:00
abstract:BACKGROUND:Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S3-S14
更新日期:2011-11-30 00:00:00
abstract:BACKGROUND:Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-319
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-381
更新日期:2012-08-08 00:00:00