Abstract:
BACKGROUND:An important subfamily of membrane proteins are the transmembrane alpha-helical proteins, in which the membrane-spanning regions are made up of alpha-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmembrane segments. The difficulty of inferring the secondary or tertiary structure of transmembrane proteins using experimental techniques has led to a surge of interest in applying techniques from machine learning and bioinformatics to infer secondary structure from primary structure in these proteins. We are therefore interested in determining which physicochemical properties are most useful for discriminating transmembrane segments from non-transmembrane segments in transmembrane proteins, and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins, and in using the results of these investigations to develop classifiers to identify transmembrane segments in transmembrane proteins. RESULTS:We determined that the most useful properties for discriminating transmembrane segments from non-transmembrane segments and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins were hydropathy, polarity, and flexibility, and used the results of this analysis to construct classifiers to discriminate transmembrane segments from non-transmembrane segments using four classification techniques: two variants of the Self-Organizing Global Ranking algorithm, a decision tree algorithm, and a support vector machine algorithm. All four techniques exhibited good performance, with out-of-sample accuracies of approximately 75%. CONCLUSIONS:Several interesting observations emerged from our study: intrinsically unstructured segments and transmembrane segments tend to have opposite properties; transmembrane proteins appear to be much richer in intrinsically unstructured segments than other proteins; and, in approximately 70% of transmembrane proteins that contain intrinsically unstructured segments, the intrinsically unstructured segments are close to transmembrane segments.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Yang JY,Yang MQ,Dunker AK,Deng Y,Huang Xdoi
10.1186/1471-2164-9-S1-S7subject
Has Abstractpub_date
2008-01-01 00:00:00pages
S7issn
1471-2164pii
1471-2164-9-S1-S7journal_volume
9 Suppl 1pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:DNA methylation is associated with aberrant gene expression in cancer, and has been shown to correlate with therapeutic response and disease prognosis in some types of cancer. We sought to investigate the biological significance of DNA methylation in lung cancer. RESULTS:We integrated the gene expression pr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1079
更新日期:2014-12-08 00:00:00
abstract:BACKGROUND:Williams syndrome transcription factor (WSTF) is a multifaceted protein that is involved in several nuclear processes, including replication, transcription, and the DNA damage response. WSTF participates in a chromatin-remodeling complex with the ISWI ATPase, SNF2H, and is thought to contribute to the mainte...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-740
更新日期:2013-10-29 00:00:00
abstract:BACKGROUND:Parasites employ proteases to evade host immune systems, feed and replicate and are often the target of anti-parasite strategies to disrupt these interactions. Myxozoans are obligate cnidarian parasites, alternating between invertebrate and fish hosts. Their genes are highly divergent from other metazoans, a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6705-y
更新日期:2020-06-16 00:00:00
abstract:BACKGROUND:Research on the aryl hydrocarbon receptor (AHR) has largely focused on variations in toxic outcomes resulting from its activation by halogenated aromatic hydrocarbons. But the AHR also plays key roles in regulating pathways critical for development, and after decades of research the mechanisms underlying phy...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1053
更新日期:2014-12-03 00:00:00
abstract:BACKGROUND:Wheat yellow (stripe) rust caused by Puccinia striiformis f. sp. tritici (PST) is one of the most devastating diseases of wheat worldwide. To design effective breeding strategies that maximize the potential for durable disease resistance it is important to understand the molecular basis of PST pathogenicity....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-270
更新日期:2013-04-22 00:00:00
abstract:BACKGROUND:Sugarcane smut, which is caused by Sporisorium scitamineum, has been threatening global sugarcane production. Breeding smut resistant sugarcane varieties has been proven to be the most effective method of controlling this particular disease. However, a lack of genome information of sugarcane has hindered the...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3146-8
更新日期:2016-10-12 00:00:00
abstract:BACKGROUND:Cadmium (Cd) is a severe detrimental environmental pollutant. To adapt to Cd-induced deleterious effects, plants have evolved sophisticated defence mechanisms. In this study, a genome-wide transcriptome analysis was performed to identify the mechanisms of Cd tolerance using two barley genotypes with distinct...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-611
更新日期:2014-07-19 00:00:00
abstract:BACKGROUND:Proliferation and tumor differentiation captured by the genomic grade index (GGI) are important prognostic indicators in breast cancer (BC) especially for the estrogen receptor positive (ER+) disease. The aims of this study were to convert this microarray index to a qRT-PCR assay (PCR-GGI), which could be re...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-424
更新日期:2009-09-10 00:00:00
abstract:BACKGROUND:The importance of transposable elements (TEs) in the genomic remodeling and chromosomal rearrangements that accompany lineage diversification in vertebrates remains the subject of debate. The major impediment to understanding the roles of TEs in genome evolution is the lack of comparative and integrative ana...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4714-x
更新日期:2018-05-09 00:00:00
abstract:BACKGROUND:Pyrethroid resistance in Anopheles funestus populations has led to an increase in malaria transmission in southern Africa. Resistance has been attributed to elevated activities of cytochrome P450s but the molecular basis underlying this metabolic resistance is unknown. Microsatellite and SNP markers were use...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-34
更新日期:2007-01-29 00:00:00
abstract:BACKGROUND:Elucidating gut microbiota among gallstone patients as well as the complex bacterial colonization of cholesterol gallstones may help in both the prediction and subsequent lowered risk of cholelithiasis. To this end, we studied the composition of bacterial communities of gut, bile, and gallstones from 29 gall...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-669
更新日期:2013-10-01 00:00:00
abstract:BACKGROUND:The steady-state behaviour of gene regulatory networks (GRNs) can provide crucial evidence for detecting disease-causing genes. However, monitoring the dynamics of GRNs is particularly difficult because biological data only reflects a snapshot of the dynamical behaviour of the living organism. Also most GRN ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-S3-S26
更新日期:2009-12-03 00:00:00
abstract:BACKGROUND:Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insight...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3465-9
更新日期:2017-01-13 00:00:00
abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5791-1
更新日期:2019-05-28 00:00:00
abstract:BACKGROUND:The Transcription Factor (TF) p63 is a master regulator of epidermal development and differentiation as evident from the remarkable skin phenotype of p63 mouse knockouts. Furthermore, ectopic expression of p63 alone is sufficient to convert simple epithelium into stratified epithelial tissues in vivo and p63...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1042
更新日期:2014-11-29 00:00:00
abstract:BACKGROUND:Genome-scale pooled CRISPR screens are powerful tools for identifying genetic dependencies across varied cellular processes. The vast majority of CRISPR screens reported to date have focused exclusively on the perturbation of protein-coding gene function. However, protein-coding genes comprise < 2% of the se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6497-0
更新日期:2020-01-31 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are short, non-coding RNAs that regulate gene expression mainly through translational repression of target mRNA molecules. More than 2700 human miRNAs have been identified and some are known to be associated with disease phenotypes and to display tissue-specific patterns of expression. ME...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3114-3
更新日期:2016-10-04 00:00:00
abstract:BACKGROUND:Meloidogyne chitwoodi commonly known as Columbia root-knot nematode or CRKN is one of the most devastating pests of potato in the Pacific Northwest of the United States of America. In addition to the roots, it infects potato tubers causing internal as well as external defects, thereby reducing the market val...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6257-1
更新日期:2019-11-28 00:00:00
abstract:BACKGROUND:The ascomycete fungus Ceratocystis cacaofunesta is the causal agent of wilt disease in cacao, which results in significant economic losses in the affected producing areas. Despite the economic importance of the Ceratocystis complex of species, no genomic data are available for any of its members. Given that ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-91
更新日期:2013-02-11 00:00:00
abstract:BACKGROUND:Duchenne muscular dystrophy (DMD), caused by mutations in the dystrophin gene, is lethal. In contrast, dystrophin-deficient mdx mice recover due to effective regeneration of affected muscle tissue. To characterize the molecular processes associated with regeneration, we compared gene expression levels in hin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-98
更新日期:2005-07-13 00:00:00
abstract:BACKGROUND:Many gram-negative bacteria use type III secretion systems (T3SSs) to translocate effector proteins into host cells. T3SS effectors can give some bacteria a competitive edge over others within the same environment and can help bacteria to invade the host cells and allow them to multiply rapidly within the ho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3363-1
更新日期:2016-12-19 00:00:00
abstract:BACKGROUND:Baculoviruses are well known for their potential as biological agents for controlling agricultural and forest pests. They are also widely used as expression vectors in molecular cloning studies. The genome sequences of 48 baculoviruses are currently available in NCBI databases. As the number of sequenced vir...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-91
更新日期:2009-02-25 00:00:00
abstract:BACKGROUND:Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-356
更新日期:2011-07-08 00:00:00
abstract:BACKGROUND:The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identificati...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-16
更新日期:2012-01-11 00:00:00
abstract:BACKGROUND:Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-351
更新日期:2009-08-03 00:00:00
abstract::As gene expression profile data from DNA microarrays accumulate rapidly, there is a natural need to compare data across labs and platforms. Comparisons of microarray data can be quite challenging due to data complexity and variability. Different labs may adopt different technology platforms. One may ask about the degr...
journal_title:BMC genomics
pub_type: 杂志文章,多中心研究
doi:10.1186/1471-2164-6-71
更新日期:2005-05-11 00:00:00
abstract:BACKGROUND:Two-component systems (TCSs) are modular and diverse signalling pathways, involving a stimulus-responsive transfer of phosphoryl groups from transmitter to partner receiver domains. TCS gene and domain organisation are both potentially informative regarding biological function, interaction partnerships and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-720
更新日期:2010-12-20 00:00:00
abstract:BACKGROUND:Microsatellites are extremely common in plant genomes, and in particular, they are significantly enriched in the 5' noncoding regions. Although some 5' noncoding microsatellites involved in gene regulation have been described, the general properties of microsatellites as regulatory elements are still unknown...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-323
更新日期:2006-12-25 00:00:00
abstract:BACKGROUND:The genomic architecture of adaptive traits remains poorly understood in non-model plants. Various approaches can be used to bridge this gap, including the mapping of quantitative trait loci (QTL) in pedigrees, and genetic association studies in non-structured populations. Here we present results on the geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-368
更新日期:2013-06-01 00:00:00
abstract:BACKGROUND:Approximately 11 Mb of finished high quality genomic sequences were sampled from cattle, dog and human to estimate genomic divergences and their regional variation among these lineages. RESULTS:Optimal three-way multi-species global sequence alignments for 84 cattle clones or loci (each >50 kb of genomic se...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-140
更新日期:2006-06-07 00:00:00