Abstract:
:Development of statistical methods has become very necessary for large-scale correlation analysis in the current "omic" data. We propose ranking analysis of correlation coefficients (RAC) based on transforming correlation matrix into correlation vector and conducting a "locally ranking" strategy that significantly reduces computational complexity and load. RAC gives estimation of null correlation distribution and an estimator of false discovery rate (FDR) for finding gene pairs of being correlated in expressions obtained by comparison between the ranked observed correlation coefficients and the ranked estimated ones at a given threshold level. The simulated and real data show that the estimated null correlation distribution is exactly the same with the true one and the FDR estimator works well in various scenarios. By applying our RAC, in the null dataset, no gene pairs were found but, in the human cancer dataset, 837 gene pairs were found to have positively correlated expression variations at FDR≤5%. RAC performs well in multiple conditions (classes), each with 3 or more replicate observations.
journal_name
Genomicsjournal_title
Genomicsauthors
Tan YDdoi
10.1016/j.ygeno.2010.09.002subject
Has Abstractpub_date
2011-01-01 00:00:00pages
58-68issue
1eissn
0888-7543issn
1089-8646pii
S0888-7543(10)00197-7journal_volume
97pub_type
杂志文章相关文献
GENOMICS文献大全abstract::Members of the solute carrier family 25 (SLC25) are known to transport molecules over the mitochondrial membrane. In this paper we present 14 novel members of SLC25 family in human. These were provided with following gene symbols by the HGNC: SLC25A32, SLC25A33, SLC25A34, SLC25A35, SLC25A37, SLC25A38, SLC25A39, SLC25A...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2006.06.016
更新日期:2006-12-01 00:00:00
abstract::MicroRNAs are small non-coding regulatory RNA molecules that play an important role in the modulation of gene expression during various environmental stresses. Pseudomonas putida RA, a plant growth promoting rhizobacteria (PGPR) colonizes the root surface of plants improving their growth and development during abiotic...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2018.01.007
更新日期:2019-07-01 00:00:00
abstract::The human CBFA2T1 (also known as MTG8) gene, on chromosome 8, has been identified through its involvement in the t(8;21) chromosomal translocation, frequently found in acute myeloid leukemia. We report here the isolation and characterization of the mouse homologue of the CBFA2T1 gene, Cbfa2t1h. Nucleotide sequence ana...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1995.9941
更新日期:1995-10-10 00:00:00
abstract::A linkage analysis with chromosome 9 markers was performed in 33 families with Friedreich ataxia (FA). Linkage with D9S15, previously established by S. Chamberlain et al. (1988, Nature London 334:248-249) was confirmed in our sample (z(theta) = 6.82 at theta = 0.02) while INFB (interferon-beta gene) shows looser linka...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(89)90323-6
更新日期:1989-01-01 00:00:00
abstract::The single functional mouse gene for MIF (macrophage migration inhibitory factor) has been cloned from a P1 library, and its exon/intron structure determined and shown to resemble that of the human gene. The gene was mapped to chromosome 10 using two multilocus crosses between laboratory strains and either Mus musculu...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1995.1070
更新日期:1995-06-10 00:00:00
abstract::We describe here a new type of X-linked liver glycogen storage disease. The main symptoms include liver enlargement and growth retardation. The clinical and biochemical abnormalities of this glycogenosis are similar to those of classical X-linked liver glycogenosis due to phosphorylase kinase deficiency (XLG). However...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1994.1322
更新日期:1994-06-01 00:00:00
abstract::Expressed sequence tags (ESTs) have been obtained from several hundred brain cDNAs as an initial effort to characterize expressed brain genes. These ESTs will become tools for human genome mapping and they will also provide candidate causative genes for inherited disorders affecting the central nervous system. We have...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(92)90439-y
更新日期:1992-03-01 00:00:00
abstract::The inheritance of obesity has been analyzed in an intercross between the lean 129/Sv mouse strain and the obesity-prone EL/Suz mouse strain. The weights of three major fat pads were determined on 4-month-old mice, and the sum of these weights, divided by body weight, was used as an adiposity index. The strategy of se...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0302
更新日期:1996-06-15 00:00:00
abstract::Uroporphyrinogen-III synthase (URO-S; EC 4.2.1.75), the fourth enzyme in the heme biosynthetic pathway, is responsible for the conversion of hydroxymethylbilane to the cyclic tetrapyrrole, uroporphyrinogen III. The deficient activity of URO-S is the enzymatic defect in congenital erythropoietic porphyria (CEP), an aut...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(95)80175-l
更新日期:1995-04-10 00:00:00
abstract::The human formylpeptide receptor (FPR) gene cluster has three members: FPR1 and FPRL1, which are expressed in neutrophils and monocytes and encode seven-transmembrane-domain chemotactic receptors specific for N-formylpeptides, and FPRL2, whose function is unknown. The FPRL1 receptor is also a lipoxin A4 receptor. Usin...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1998.5376
更新日期:1998-07-15 00:00:00
abstract::Balanced reciprocal translocation carriers are usually phenotypically normal but are at an increased risk of infertility, recurrent miscarriage or having affected children. Preimplantation genetic testing on chromosomal structural rearrangement (PGT-SR) offers a way to screen against unbalanced embryos. Here, we demon...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2019.04.001
更新日期:2020-01-01 00:00:00
abstract::We have isolated a human homologue (MEST) of the mouse mesoderm-specific transcript (Mest) gene that shares about 70% nucleotide sequence homology. Northern blot analysis showed that the MEST gene was expressed in all major fetal organs and tissues so far examined, i.e., amnion, brain, heart, lung, stomach, gut, adren...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0502
更新日期:1996-09-15 00:00:00
abstract::Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the c...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2016.01.003
更新日期:2016-05-01 00:00:00
abstract::The Xist sequence has been proposed as a potential candidate for the X-inactivation center based both on its localization within the candidate region for the X-inactivation center in man and mouse and on its unique pattern of expression from the inactive X chromosome. We have cloned 550 kb of DNA surrounding the mouse...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1993.1108
更新日期:1993-03-01 00:00:00
abstract::Genes homologous to those located on human chromosome 4 (HSA4) were mapped in the bovine to determine regions of syntenic conservation among humans, mice, and cattle. Previous studies have shown that two homologs of genes on HSA4, PGM2 and PEPS, are located in bovine syntenic group U15 (chromosome 6). The homologous m...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(05)80295-2
更新日期:1992-09-01 00:00:00
abstract::The microtubule-associated protein 1B (MAP1B) locus has been mapped in close proximity to spinal muscular atrophy (SMA) on chromosome 5q13. We have identified a second microsatellite within a MAP1B intron, which increases the heterozygosity of this locus to 94%. Two unambiguous recombination events establish MAP1B as ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(92)90012-h
更新日期:1992-08-01 00:00:00
abstract::Familial hemiplegic migraine (FHM) is a distinctive form of migraine with an autosomal dominant mode of inheritance. The migraine-like attacks are associated with transient hemiparesis. A locus for FHM has recently been assigned to chromosome 19 by linkage mapping. In the present study, five unrelated pedigrees with m...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1994.1340
更新日期:1994-07-01 00:00:00
abstract::Abnormal histone modifications (HMs) and transcription factors (TFs) can alter the expression of cancer-related genes to promote tumorigenesis. We studied the variations of 11 HMs and 2 TFs in human breast cancer cells (MCF-7) compared to human normal mammary epithelial cells (HMEC), and the effects of HMs/TFs in vari...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2019.05.026
更新日期:2020-01-01 00:00:00
abstract::The closely linked proline-rich protein (Prp) genes, coding for abundant salivary proteins, are located on distal mouse chromosome 6. They are part of a conserved linkage group that is represented on human chromosome 12p. Two other markers, Ea-10 and Es-12, that were previously unassigned to a chromosome are closely l...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/0888-7543(89)90004-9
更新日期:1989-10-01 00:00:00
abstract::CancerEnD is an integrated resource developed for annotating 8524 unique expressed enhancers, associated genes, somatic mutations and copy number variations of 8063 cancer samples from 18 cancer types of TCGA. Somatic mutation data was taken from the COSMIC repository. To delineate the relationship of change in copy n...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2020.04.028
更新日期:2020-09-01 00:00:00
abstract::The proximal albino deletions identify several functional regions on mouse Chromosome 7 critical for differentiation of mesoderm (mesd), development of the hypothalamus neuroendocrine lineage (nelg), and function of the liver (hsdr1). Using comparative mapping and genomic sequence analysis, we have identified four nov...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.2000.6466
更新日期:2001-02-15 00:00:00
abstract::The cDNA for the PSST subunit of human mitochondrial nicotinamide adenine dinucleotide (NADH): ubiquinone oxidoreductase [complex I; NADH dehydrogenase (ubiquinone), Fe-S (20 kDa); EC 1.6.5.3] was generated by polymerase chain reaction (PCR) amplification of human cDNA. The sequence of the mature protein deduced from ...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1996.0572
更新日期:1996-11-01 00:00:00
abstract::Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2011.07.005
更新日期:2011-11-01 00:00:00
abstract::Paulownia tomentosa is an important foundation forest tree species in semiarid areas. The lack of genetic information hinders research into the mechanisms involved in its response to abiotic stresses. Here, short-read sequencing technology (Illumina) was used to de novo assemble the transcriptome on P. tomentosa. A to...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2014.08.008
更新日期:2014-10-01 00:00:00
abstract::A novel method for identifying DNA point mutations has been developed by using mismatch repair enzymes. The high specificity of the Escherichia coli MutY protein has permitted the development of a reliable and sensitive method for the detection and characterization of point mutations in the human genome. The MutY prot...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(05)80213-7
更新日期:1992-10-01 00:00:00
abstract::Cataract Tohoku (Cat(Tohm)) is a dominant cataract mutation that leads to severe degeneration of lens fiber cells. Linkage analysis showed that the Cat(Tohm) mutation is located on mouse chromosome 10, close to the gene for aquaporin-0 (Aqp0), which encodes a membrane protein that is expressed specifically in lens fib...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/s0888-7543(03)00029-6
更新日期:2003-04-01 00:00:00
abstract::We have isolated and examined the gene for the heart isoform of cytochrome c oxidase subunit VIIa (COX VIIa-H) in mouse, an isoform gene previously thought to be lacking in rodents. Interspecies amino acid comparisons indicate that mouse COX VIIa-H protein displays 82.5 and 70.9% identity with the bovine and human hea...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1998.5279
更新日期:1998-05-01 00:00:00
abstract::There is abundant evidence that the DNA in eukaryotic cells is organized into loop domains that represent basic structural and functional units of chromatin packaging. To explore the DNA domain organization of the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1, we have identified a significant...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2006.11.003
更新日期:2007-03-01 00:00:00
abstract::The rat HNF-3 (hepatocyte nuclear factor 3) gene family encodes three transcription factors known to be important in the regulation of gene expression in liver and lung. We have cloned and characterized the mouse genes and cDNAs for HNF-3 alpha, beta, and gamma and analyzed their expression patterns in various adult t...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1006/geno.1994.1191
更新日期:1994-04-01 00:00:00
abstract::Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletel...
journal_title:Genomics
pub_type: 杂志文章
doi:10.1016/j.ygeno.2018.01.011
更新日期:2019-03-01 00:00:00