As a statistical method integrating multi-features and multi-data, meta-analysis was introduced to the field of life science in the 1990s. With the rapid advances in high-throughput technologies, life omics, the core of which are genomics, transcriptomics and proteomics, is becoming the new hot spot of life science. Although the fast output of massive data has promoted the development of omics study, it results in excessive data that are difficult to integrate systematically. In this case, meta-analysis is frequently applied to analyze different types of data and is improved continuously. Here, we first summarize the representative meta-analysis methods systematically, and then study the current applications of meta-analysis in various omics fields, finally we discuss the still-existing problems and the future development of meta-analysis.
Genomics ; Meta-Analysis as Topic ; Proteomics ; Statistics as Topic

With the rapid development of genome sequencing technologies, a large amount of prokaryote genomes have been sequenced in recent years. To further investigate the models and functions of genomes, the algorithms for genome annotations based on the sequence and homology features have been widely implemented to newly sequenced genomes. However, gene annotations only using the genomic information are prone to errors, such as the incorrect N-terminals and pseudogenes. It is even harder to provide reasonable annotating results in the case of the poor genome sequencing results. The transcriptomics based on the technologies such as microarray and RNA-seq and the proteomics based on the MS/MS have been used widely to identify the gene products with high throughput and high sensitivity, providing the powerful tools for the verification and correction of annotated genome. Compared with transcriptomics, proteomics can generate the protein list for the expressed genes in the samples or cells without any confusion of the non-coding RNA, leading the proteogenomics an important basis for the genome annotations in prokaryotes. In this paper, we first described the traditional genome annotation algorithms and pointed out the shortcomings. Then we summarized the advantages of proteomics in the genome annotations and reviewed the progress of proteogenomics in prokaryotes. Finally we discussed the challenges and strategies in the data analyses and potential solutions for the developments of proteogenomics.
Genomics ; Molecular Sequence Annotation ; Prokaryotic Cells ; metabolism ; Proteomics ; Tandem Mass Spectrometry

Objective China has the biggest population of commonly encountered liver diseases , so hepatology resear-ches are of great importance to human health .In order to comprehensively collect/organize and effectively share/display liv-er physiopathology knowledge scattered around databases and literature , a Human Liver Disease Ontology ( HuLDO ) is built and applied in many ways .Methods HuLDO systematically classified and annotated various human liver diseases based on extensive cross mapping and integration of several authoritative nomenclatures of diseases and two monographs of hepatology .Results In the present version , HuLDO encompassed knowledge of 227 human liver diseases and was enriched by plenty of synonyms,definitions, descriptions, references, and logical or pathological relations between different disea-ses.Compared with other existing nomenclatures , HuLDO extended far beyond them in the scope of liver diseases .Several applications of HuLDO in database construction , knowledge collection and text mining were also described .Conclusion HuLDO offers a sound basis for knowledge mining , data integration and data analysis in the field of hepatology .HuLDO is publicly available at ftp://liveratlas.hupo.org.cn/5.liver 5.liver%20Disease%20Ontology/.

The combination of tandem spectrometry and database searching is one of the most popular technologies for protein identification.However,only those proteins in the searching database could be identified,and current database is far from completeness.So it is necessary to mining the MS/MS data comprehensively,in which novel protein identification is the most important one.The definition of novel protein could be divided into three levels according to their annotations of sequences and functions.As a part of protein identification,the main approaches used to identify novel protein are basing on the following two different ways:de novo sequencing combined with similarity search and searching against nucleotide acid databases such as EST or genome databases.Several mature or newly developed methods and techniques were summarized,and the problems and strategies discussed here would be helpful for the related researches.

Objective:To explore the lactate metabolism in brain tissue of the mice with early acute hypoxia-ischemia injury,and to provide data support for 9.4T 1 H-NMR spectroscopy in detecting the lactate level clinically.Methods:Eighty Kunming mice were randomly divided into sixteen groups (0 s,20 s,40 s,60 s,2 min,4 min, 6 min,8 min, 10 min, 12 min, 14 min, 16 min, 18 min,and 20 min)according to the duration of hypoxia-ischemia (n=5).The changes of lactate levels were detected by 9.4T 1 H-NMR spectroscopy. Results:After the initiation of hypoxia-ischemia injury,the lactate level began to increase rapidly to the highest value of (6.89 ± 0.34)μmol·g-1 at 20 s,then started to decline quickly from 40 s to 2 min,and eventually decreased to a stable level of (4.85±0.36)μmol·g-1 until 6 min.Compared with control group,the levels of lactate in brain tissue of the mice in hypoxic-ischemic groups were increased (P <0.01).Conclusion:40 s of acute hypoxia-ischemia may be the lactate cerebral neuron threshold during the anaerobic glycolysis. 9.4T1 H-MRS can provide the exact time window for detecting the lactate metabolism.

OBJECTIVE:To evaluation of the efficacy and safety of azithromycin in the treatment of acute infections METHODS:A randomized controlled multicenter clinical study was used to compare the clinical efficacy of azithromycin(200mg q d for 3～5 days) with erythromycin(500mg b i d for 5 days) RESULTS:The cure rate,effective rate,and bacterial clearance rate were 76 7%,95 0%,and 94 3% respectively for azithromycin group and were 48 3%,76 7%,and 77 4% respectively for erythromycin group with a side-effect incidence of 10 0% for azithromycin group and 39 3% for erythromycin group CONCLUSION:Azithromycin is superior to erythromycin in clinical efficacy,safety and side-effect incidence

As the complexity of samples and experimental processes, the repeatability of mass spectrometry experiments is still not satisfactory, the results of peptide identification and quantification show high randomicity), the probability of peptide being detected by mass spectrometry in proteome research, especially in quantitative proteomic study, has received much attention. Therefore, a lot of experimental researches have been done, as well as a number of computational prediction methods have been developed. In this article, we summarized the important factors impacting the peptide detectability, investigated the existing prediction methods) and reviewed their applications in experimental study.

Objective To evaluate the effect of continuous aspiration of subglottic secretions (CASS) on the prevention of ventilator-associated pneumonia (VAP) in mechanically ventilated patients. Methods Patients ventilated mechanically at the ICU from October, 2004 to April,2006 were randomly divided into 2 groups: one group received CASS and the other did not (NASS group). CASS was performed immediately after admission for patients in the CASS group. The diagnosis d VAP was made based on clinical presentations, and the evaluation of YAP was done using simplified version of the clinical pulmonary infection score (CPIS). The general status of the patients, days of ventilated treatment, the volume of daily aspirated aubglottic secretions, the morbidity and timing of VAP, days of stay in ICU and mortality within 28 days of hospitalization were recorded. Results One hundred and one patients were included in the study. There were 48 patients in the CASS group who were treated with mechanical ventilation more than 48 hours,and 43 patients in the NASS group. There was no significant difference in the general status of the patients and days of ventilation between 2 groups with the averaged score of APACHE Ⅱ being 20.8± 6.1. The average of CPIS was of 5.6±1.0 when VAP was diagnosed. The mean volume of aspirated subglottic secretions within the first 24 hours in the CASS group (n=48) was (27.2±21.2)ml. The morbidity of VAP in the CASS and the NASS groups was 25.0% and 46. 5% respectively (P=0.032), and the length of time before the onset of VAP in these 2 groups was (7.3±4.2) days and (5.1±3.0) days respectively (P=0.100). There was a significant increase in the percentage of gram-positive cocci from the lower respiratory tracts in the NASS group compared with that in the CASS group (P=0.004). In the CASS group, the volume of the first daily aspirated subglottic secretions in patients with VAP was significantly less than that in patients without VAP(P =0.006). The morbidity of VAP in patients with failed early aspiration (the volume of first daily aspirated secretions≤20 ml) was significantly higher than that in patients in whom the aspiration was effective (P<0.01). The length of mechanical ventilation in patients with VAP was significantly longer than that in patients without VAP(P=0.000). The in-hospital mortality in patients with VAP was significantly higher than that in patients without VAP(P=0.009), and the mortality in 28 days after admission in patients with VAP was significantly higher than that in patients without VAP(P=0.035).Conclusion Effective continuous aspiration of subglottic secretions could significantly reduce the morbidity of early-onset VAP.

Data analysis poses a significant challenge to the large-scale proteomics studies. Based on the structured and controlled vocabularies-Gene Ontology (GO), and the GO annotation from related databases, a strategy composed of several programs and local databases is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration. This strategy has been successfully used in the Human Fetal Liver (HFL) proteomic research, which is available online at http://www.hupo.org.cn/GOfact/.

Aim To evaluate the time-course curve of expression of TRPC1 and vascular tone of pulmonary arteries(PAs)mediated by SOCE in chronic hypoxia pulmonary hyperte-nsion rats.Methods Both tension of PA rings and expression of TRPC1 were tested in CH exposure (1 0.0 % ±0.5 %partialpressure ofoxygen ) induced pulmonary hypertensive (PH)rats,and the time-course curve(detected respectively in CH 1 ,3,5, 7,1 4,21 d)was traced.Results ①CH could up-regulate the mean right ventricular pressure(mRVSP) ,which was increased significantly on 1 d,and reached the maximum on 7d;right ventricular weight index (RV-MI)began increase on 3d,and kept rising;②semi-quantitative reverse transcription polyme-rase chain reaction (RT-PCR)was performed to detect the expression of TRPC1 in PAs.The expression of TRPC1 increased significantly on 1 d,and reached the maxi-mum on 3d;③CH could up-regulate the vascular tone of PAs mediated by SOCE,which was increased signif-icantly on 3d,and reached the maximum on 7d.Con-clusions TRPC1 /SOCE increases significantly in the early days of CH,and the time-course curve of the two has correlation,which reflects the important role of the upregulation of TRPC1 /SOCE in the process of chronic hypoxia pulmonary hypertension.