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101.
Andrew J Holloway Alicia Oshlack Dileepa S Diyagama David DL Bowtell Gordon K Smyth 《BMC bioinformatics》2006,7(1):1-20
Background
It is one of the ultimate goals for modern biological research to fully elucidate the intricate interplays and the regulations of the molecular determinants that propel and characterize the progression of versatile life phenomena, to name a few, cell cycling, developmental biology, aging, and the progressive and recurrent pathogenesis of complex diseases. The vast amount of large-scale and genome-wide time-resolved data is becoming increasing available, which provides the golden opportunity to unravel the challenging reverse-engineering problem of time-delayed gene regulatory networks.Results
In particular, this methodological paper aims to reconstruct regulatory networks from temporal gene expression data by using delayed correlations between genes, i.e., pairwise overlaps of expression levels shifted in time relative each other. We have thus developed a novel model-free computational toolbox termed TdGRN (Time-delayed Gene Regulatory Network) to address the underlying regulations of genes that can span any unit(s) of time intervals. This bioinformatics toolbox has provided a unified approach to uncovering time trends of gene regulations through decision analysis of the newly designed time-delayed gene expression matrix. We have applied the proposed method to yeast cell cycling and human HeLa cell cycling and have discovered most of the underlying time-delayed regulations that are supported by multiple lines of experimental evidence and that are remarkably consistent with the current knowledge on phase characteristics for the cell cyclings.Conclusion
We established a usable and powerful model-free approach to dissecting high-order dynamic trends of gene-gene interactions. We have carefully validated the proposed algorithm by applying it to two publicly available cell cycling datasets. In addition to uncovering the time trends of gene regulations for cell cycling, this unified approach can also be used to study the complex gene regulations related to the development, aging and progressive pathogenesis of a complex disease where potential dependences between different experiment units might occurs. 相似文献102.
Clifford DL Folmes Grzegorz Sawicki Virgilio JJ Cadete Grant Masson Amy J Barr Gary D Lopaschuk 《Proteome science》2010,8(1):38
Background
During and following myocardial ischemia, glucose oxidation rates are low and fatty acids dominate as a source of oxidative metabolism. This metabolic phenotype is associated with contractile dysfunction during reperfusion. To determine the mechanism of this reliance on fatty acid oxidation as a source of ATP generation, a functional proteomics approach was utilized. 相似文献103.
A nuclear gene for higher level phylogenetics: phosphoenolpyruvate carboxykinase tracks mesozoic-age divergences within Lepidoptera (Insecta) 总被引:3,自引:0,他引:3
The sequence of phosphoenolpyruvate carboxykinase (PEPCK) has been
previously identified as a promising candidate for reconstructing
Mesozoic-age divergences (Friedlander, Regier, and Mitter 1992, 1994). To
test this hypothesis more rigorously, 597 nucleotides of aligned PEPCK
coding sequence (approximately 30% of the coding region) were generated
from 18 species representing Mesozoic-age lineages of moths (Insecta:
Lepidoptera) and outgroup taxa. Relationships among basal Lepidoptera are
well established by morphological analysis, providing a strong test for the
utility of a gene which has not previously been used in systematics.
Parsimony and other phylogenetic analyses were conducted on nucleotides by
codon positions (nt1, nt2, nt3) separately and in combination, and on amino
acids, for comparison to the test phylogeny. The highest concordance was
achieved with nt1 + nt2, for which one of two most-parsimonious trees was
identical to the test phylogeny, and with all nucleotides when nt3 was
down-weighted sevenfold or higher, for which a single most-parsimonious
tree identical to the test phylogeny resulted. Substitutions in nt3
approached saturation in many, but not all, pairwise comparisons and their
exclusion or severe downweighting greatly increased the degree of
concordance with the test phylogeny. Neighbor-joining analysis confirms
this finding. The utility of PEPCK for phylogenetics is demonstrated over a
time span for which few other suitable genes are currently available.
相似文献
104.
Louis Shattuck Baer 《The Western journal of medicine》1957,87(2):104-107
For dealing economically yet effectively with patients who are being made sick by psychic burdens rather than by “simple” organic disease, a trained interviewer who follows a formal outline in obtaining information from patients, can be of great assistance.The physician who makes use of the services of such an interviewer should select a person with good qualifications for the job and then train her for it. It is also up to the physician to get the patient to accept the idea of interview by such an assistant.After the interview, the interviewer prepares a typewritten summary for the physician for use as a guide in discussing means of treatment and prevention of psychosomatic illness with the patient.The method saves the physician much time, the patients much money, and has resulted in many gratifying therapeutic successes. 相似文献
105.
Andrew J Holloway Alicia Oshlack Dileepa S Diyagama David DL Bowtell Gordon K Smyth 《BMC bioinformatics》2006,7(1):511
Background
Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for these technologies on a whole-array basis. 相似文献106.
107.
108.
An effective method of DNA isolation from the mature leaves of Gossypium species that contain large amounts of phenolic terpenoids and tannins 总被引:3,自引:0,他引:3
Purified and unstained nuclei were isolated from the leaves of several Gossypium species (diploid and tetraploid) by means of a citrate buffer (pH 5.0), Triton X-100 (5%), and a reducing sugar (1M glucose). DNA, previously unobtainable, was then extracted from the nuclei by conventional means. Comparisons of final DNA yield were made between three methods of purification: namely, the standardized ribonuclease procedure, hydroxyapatite chromatography and equilibrium density centrifugation in cesium chloride. The latter method produce the lowest, yet purest, yield of DNA for renaturation studies in Gossypium. 相似文献
109.
110.