Different normalization strategies for microarray gene expression traits affect the heritability estimation

Abstract Several studies have been conducted to assess the influence of genetic variation on genome-wide gene expression profiles measured by the microarray technologies. Due to substantial noise in microarray-based experiments, it has long been recognized that proper normalization is a crucial step to ensure sensitive and reliable downstream analyses. This is especially true when large number of samples were collected and analyzed. In this study, we investigated the impact of different normalization strategies on genome wide linkage analyses, in particular, the estimation of heritability of gene expression traits. We used the Genetics Analysis Workshop 15 Problem 1 data. We found that there are significant differences in the estimated number of genes showing heritability when different normalization strategies were used. RMA (robust multiarray average) and dChip identify 45% and 13% more genes showing heritability than MAS 5.0, respectively. Our study also reveals that a large number of genes show strong "family effect" in their expression levels but no significant heritability. Analysis of their annotation indicates different types of genes were enriched in this group compared to genes showing strong heritability.http://deepblue.lib.umich.edu/bitstream/2027.42/117370/1/12919_2007_Article_2518.pd

Structural comparison of metabolic networks in selected single cell organisms

BACKGROUND: There has been tremendous interest in the study of biological network structure. An array of measurements has been conceived to assess the topological properties of these networks. In this study, we compared the metabolic network structures of eleven single cell organisms representing the three domains of life using these measurements, hoping to find out whether the intrinsic network design principle(s), reflected by these measurements, are different among species in the three domains of life. RESULTS: Three groups of topological properties were used in this study: network indices, degree distribution measures and motif profile measure. All of which are higher-level topological properties except for the marginal degree distribution. Metabolic networks in Archaeal species are found to be different from those in S. cerevisiae and the six Bacterial species in almost all measured higher-level topological properties. Our findings also indicate that the metabolic network in Archaeal species is similar to the exponential random network. CONCLUSION: If these metabolic network properties of the organisms studied can be extended to other species in their respective domains (which is likely), then the design principle(s) of Archaea are fundamentally different from those of Bacteria and Eukaryote. Furthermore, the functional mechanisms of Archaeal metabolic networks revealed in this study differentiate significantly from those of Bacterial and Eukaryotic organisms, which warrant further investigation

Spectral Properties From Lyman-alpha to H-alpha For An Essentially Complete Sample of Quasars I: Data

We have obtained quasi-simultaneous ultraviolet-optical spectra for 22 out of 23 quasars in the complete PG-X-ray sample with redshift, z<0.4, and M_B<-23. The spectra cover rest-frame wavelengths from at least Lyman-alpha to H-alpha. Here we provide a detailed description of the data, including careful spectrophotometry and redshift determination. We also present direct measurements of the continua, strong emission lines and features, including Lyman-alpha, SiIV+OIV], CIV, CIII], SiIII], MgII, H-beta, [OIII], He5876+NaI5890,5896, H-alpha, and blended iron emission in the UV and optical. The widths, asymmetries and velocity shifts of profiles of strong emission lines show that CIV and Lyman-alpha are very different from H-beta and H-alpha. This suggests that the motion of the broad line region is related to the ionization structure, but the data appears not agree with the radially stratified ionization structure supported by reverberation mapping studies, and therefore suggest that outflows contribute additional velocity components to the broad emission line profiles.Comment: 42 pages, 10 figures, 13 tables. Accepted by AJ. Supplemental figures not included. Full version available at http://physics.uwyo.edu/~shang/pgxpaper/ShangPaper.pd

GDGT Distribution in a Stratified Lake and Implications for the Application of TEX86 in Paleoenvironmental Reconstructions

We investigated the relationship between distributions of GDGTs, GDGT-based proxies and environmental factors in a stratified lake in northwestern Norway. More than 90% of isoGDGTs were produced at the bottom of the oxycline, indicating a predominance of ammonia-oxidizing Group I.1a of Thaumarchaeota, supported by high crenarchaeol/caldarchaeol ratios. Dissolved oxygen content, rather than temperature, exercised a primary control on TEX86 values. In spite of low BIT value in surface sediment, the reconstructed lake surface temperature was “cold” biased. MBT values in streams and lake surface water were significantly smaller than those in the catchment soil, suggesting in situ production of brGDGTs in streams. A rapid transition of MBT vs. temperature/pH relationships occurring at the bottom of oxycline indicated the differential production of various brGDGTs with D.O. and depths. Only within the oxycline were CBT-based pH values close to in situ pH. Our results confirm earlier studies calling for caution in applying TEX86 as a surface temperature proxy, or MBT and/or CBT for reconstructing pH, in anoxic or euxinic lakes, estuaries and ocean basins. We propose that caldarchaeol/crenarchaeol ratio, an indicator of contributions from methanogenic archaea, together with the BIT and TEX86 proxies, can help reconstruct past levels of stratification

Outflows and the Physical Properties of Quasars

We have investigated a sample of 5088 quasars from the Sloan Digital Sky Survey Second Data Release in order to determine how the frequency and properties of broad absorptions lines (BALs) depend on black hole mass, bolometric luminosity, Eddington fraction (L/L_Edd), and spectral slope. We focus only on high-ionization BALs and find a number of significant results. While quasars accreting near the Eddington limit are more likely to show BALs than lower $L/L_{Edd}$ systems, BALs are present in quasars accreting at only a few percent Eddington. We find a stronger effect with bolometric luminosity, such that the most luminous quasars are more likely to show BALs. There is an additional effect, previously known, that BAL quasars are redder on average than unabsorbed quasars. The strongest effects involving the quasar physical properties and BAL properties are related to terminal outflow velocity. Maximum observed outflow velocities increase with both the bolometric luminosity and the blueness of the spectral slope, suggesting that the ultraviolet luminosity to a great extent determines the acceleration. These results support the idea of outflow acceleration via ultraviolet line scattering.Comment: Uses emulateapj.cls, 14 pages including 7 tables and 7 figures. Accepted for publication in the Astrophysical Journal, Unabridged version of Table 4 can be downloaded from http://physics.uwyo.edu/agn

A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks

Abstract Background The large amount of literature in the post-genomics era enables the study of gene interactions and networks using all available articles published for a specific organism. MeSH is a controlled vocabulary of medical and scientific terms that is used by biomedical scientists to manually index articles in the PubMed literature database. We hypothesized that genome-wide gene-MeSH term associations from the PubMed literature database could be used to predict implicit gene-to-gene relationships and networks. While the gene-MeSH associations have been used to detect gene-gene interactions in some studies, different methods have not been well compared, and such a strategy has not been evaluated for a genome-wide literature analysis. Genome-wide literature mining of gene-to-gene interactions allows ranking of the best gene interactions and investigation of comprehensive biological networks at a genome level. Results The genome-wide GenoMesh literature mining algorithm was developed by sequentially generating a gene-article matrix, a normalized gene-MeSH term matrix, and a gene-gene matrix. The gene-gene matrix relies on the calculation of pairwise gene dissimilarities based on gene-MeSH relationships. An optimized dissimilarity score was identified from six well-studied functions based on a receiver operating characteristic (ROC) analysis. Based on the studies with well-studied Escherichia coli and less-studied Brucella spp., GenoMesh was found to accurately identify gene functions using weighted MeSH terms, predict gene-gene interactions not reported in the literature, and cluster all the genes studied from an organism using the MeSH-based gene-gene matrix. A web-based GenoMesh literature mining program is also available at: http://genomesh.hegroup.org. GenoMesh also predicts gene interactions and networks among genes associated with specific MeSH terms or user-selected gene lists. Conclusions The GenoMesh algorithm and web program provide the first genome-wide, MeSH-based literature mining system that effectively predicts implicit gene-gene interaction relationships and networks in a genome-wide scope.http://deepblue.lib.umich.edu/bitstream/2027.42/112478/1/12918_2013_Article_1166.pd