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

[Objective] To find the method of pharmacokinetics experiment about Huanglianjiedu Decoction.[Methods] According to references about pharmacokinetics experiments on Huanglianjiedu Decoction,the article summarized the achievements in quantitative analysis,the influence of distill techniques and pharmacokinetics on indict components in Huanglianjiedu Decoction.This article attached importance to applying the technologies of PK-PD modeling and Data Mining in research of Chinese traditional medicine compound.[Conclusion] The pharmacokinetics study on Huanglianjiedu Decoction is just in the first step; thereby further studies will be taken on this decoction in order to reveal the active fractions and effect mechanism.

Objective To evaluate clinical efficacy and survival outcomes of neoadjuvant treatment on early stage bulky cervical carcinoma.Methods A total of 155 cases with bulky stage Ⅰ b2 or Ⅱ a2 cervical carcinoma in Affiliated Tumor Hospital of Shantou University Medical College from Nov.2010 to Feb.2015 was reviewed and divided into two groups according to pre-operative treatment 108 cases in the neoadjuvant treatment group and 47 cases in the control group who underwent radical surgery directly.The clinical,pathologic,and follow-up data were analyzed retrospectively.Results The total response rate of neoadjuvant treatment was 75.0％.Histological grade in neoadjuvant treatment group was better than the other group and the rate of deep myometrial infiltration was tend to low in neoadjuvant treatment group.There was no difference in pathological type,parametrial involvement,lymph node metastasis,and lymph vascular space invasion between two groups.The rate of postoperative treatment was similar (92.6％ vs 87.2％,P ＞ 0.05).The overall survival rate of neoadjuvant treatment group was 96.4％ and the other group was 88.9％ (P =0.069).Conclusions Neoadjuvant treatment was effective for early stage bulky cervical carcinoma.It might reduce tumor histological grade and maybe improve the overall survival of patients.

Objective To explore the value of serum CA125 level to the prognosis of epithelial ovarian cancer.Methods The clinicopathologic data and serum CA125 level of 76 patients with epithelial ovarian cancer from Jan.2003 to Dec.2009 were analyzed retrospectively, and the outcomes of patients were followed up.Results No relationship was found between CA125 concentration before therapy with prognosis and cytoreductive condition for epithelial ovarian cancer.The normal or abnormal CA125 concentration after 3 courses of treatment meant different prognosis, with the 5-year survival rates of 63.8 ％ and 25.0 ％, and the median survival time of 57 months and 28 months, respectively (x2 =19.951, P =0.000).The 5-year survival rates of patients with CA125 concentration≤ 10.0 U/ml and＞10.0 U/ml after therapy were 72.7 ％ and 42.8 ％, respectively (x2 =7.266, P =0.007).According to multivariate Cox proportional-hazard model, two independent factors , operative pathological staging and CA125 concentration after 3 courses, were related significantly to the prognosis of epithelial ovarian cancer (P ＜ 0.05).Conclusion Serum CA125 level, especially after 3 courses and therapy, plays an important role in the prognosis of epithelial ovarian cancer.

Objective:In the operation of esophageal cancer, nano carbon suspension was used for lymph tracing, and the effect of lymph tracing in different regions and its influence on prognosis were analyzed.Methods:From July 2013 to August 2014, 100 patients under esophageal cancer surgery in our department were analyzed. Randomly divided into experimental group and control group, 50 cases each. During the operation, nano carbon suspension was used to trace the lymph nodes in the experimental group, while conventional operation was only used in the control group. The general baseline data, the number of lymph nodes and positive lymph nodes in each region in the two groups were compared, the lymph node metastasis and survival were followed up, and the prognosis of the two groups were compared.Results:There was no significant difference in baseline data between the two groups( P>0.05). The average number of lymph nodes in the experimental group was 18.6 per case, and that in the control group was 15.1 per case. There was significant difference between the two groups( P=0.003). There was no significant difference in the number and degree of metastasis between the two groups( P=0.233, P=0.463). The effect of nano carbon suspension on tracing lymph nodes around the lower mediastinal esophagus was better. In the experimental group, 4.38 lymph nodes were removed in this area on average, 0.34 of which were metastatic lymph nodes. In the control group, 2.52 lymph nodes were removed in each case on average, 0.10 of which were metastatic lymph nodes. The comparison between the two groups was significantly higher than that of the control group( P=0.001, P=0.011 respectively). In the upper mediastinum, abdominal cavity and other mediastinal lymph nodes, there was no significant difference in the number of lymph nodes, the number of lymph nodes and the degree of metastasis between the two groups( P>0.05). The time of lymph node metastasis in the experimental group was significantly later than that in the control group( P=0.048, log rank test). There was no significant difference in survival time between the two groups( P=0.692, log rank test) . Conclusion:The results show that the nano carbon suspension has a good effect on the lymph node tracing during the operation of esophageal cancer, and the effect on the lymph node tracing around the lower mediastinal esophagus is better.In the area close to the lung drainage area, the tracer effect is poor, and it has certain effect in reducing or delaying lymph node metastasis.

Objective To evaluate the clinicopathological characteristics and prognosis of cervical adenocarcinoma patients with stage Ⅰ b1-Ⅱ b treated with radical hysterectomy and systematic lymphadenectomy.Methods The clinical,pathologic and follow-up data of 118 cases of cervical adenocarcinoma with stage Ⅰ b1-Ⅱ b treated with radical hysterectomy and systematic lymphadenectomy in Cancer Hospital of Shantou University Medical College from Dec.2003 to Nov.2015 were analyzed retrospectively.Results 118 patients of cervical adenocarcinoma with stage Ⅰ b1-Ⅱ b had a median age of 46 years at diagnosis.28 cases were postmenopausal and 90 cases were premenopausal.There were 77 cases in phase Ⅰ b1,25 in stage Ⅰ b2,4 in stage Ⅱ a1,7 in stage Ⅱ a2,5 in stage Ⅱ b.The rate of ovarian metastasis was 3.39％.The 3-year recurrence-free survival rate of the patients was 81.6％.The 3-year overall survival rate of the patients was 83.9％,and 89.10％ for stage Ⅰ b1,73.7％for stage Ⅰ b2,100％ for stage Ⅱ a1,83.3％ for stage Ⅱ a2,60.0％ for stage Ⅱ b.The 3-year overall survival rates of the patients who receive non-chemoradiotherapy,chemotherapy,radiotherapy and chemoradiotherapy after operation were 90.6％,100％,84.6％ and 70％ respectively.The result of Cox proportional hazards regression model analysis indicated that lymph lode metastasis and ovarian metastasis was the independent prognostic factor of desease-free survival,ovarian metastasis and deep myometrial invasion was the independent prognostic factor of overall survival.Conclusions Premenopausal cases are more common than postmenopausal cases in cervical adenocarcinoma with stage Ⅰ b1-Ⅱ b.Ovarian presevation is feasible for early-stage cervical denocarcinoma after full assessment.Pelvic irradiation with concurrent chemotherapy can lead a better prognosis for the patients with pathological risk factors.

With the development of mass spectrometry technologies and bioinformatics analysis algorithms, disease research-driven human proteome project (HPP) is advancing rapidly. Protein biomarkers play critical roles in clinical applications and the biomarker discovery strategies and methods have become one of research hotspots. Feature selection and machine learning methods have good effects on solving the "dimensionality" and "sparsity" problems of proteomics data, which have been widely used in the discovery of protein biomarkers. Here, we systematically review the strategy of protein biomarker discovery and the frequently-used machine learning methods. Also, the review illustrates the prospects and limitations of deep learning in this field. It is aimed at providing a valuable reference for corresponding researchers.
Algorithms ; Biomarkers ; Humans ; Machine Learning ; Mass Spectrometry ; Proteomics

Objective    To investigate the value of esophageal activity examination under X-ray fluoroscopy and chest CT in evaluating the resectability of upper thoracic esophageal cancer. Methods    A total of 221 upper thoracic esophageal carcinoma patients underwent radical operation between 2009 and 2015 in our hospital were enrolled, including 141 males and 80 females with a median age of 59 (47-79) years. Preoperative routine esophageal activity examination under X-ray fluoroscopy and chest enhanced CT were performed to determine whether the tumor had external invasion. The results of the two methods were compared with that observed during the operation. Results    The number of patients with esophageal activity score 1-6 was 70, 85, 32, 29, 2 and 3, respectively. The area under the receiver operating characteristic (ROC) curve (AUC) of esophageal activity examination was 0.897 (95%CI 0.85-0.93, P<0.001), and the cut off value was >3. According to the ROC curve activity score, 4-6 points were considered as invasion, and 1-3 points were non-invasion. The sensitivity, specificity, accuracy and misdiagnosis rate of esophageal activity examination was 75.0%, 89.3%, 88.2%, 10.7%, respectively, and those of CT scan were 75.0%, 66.8%, 67.4%, 33.2%, respectively. Compared with CT scan, the specificity of esophageal activity examination was higher and the misdiagnosis rate was lower. Compared with the detection during the operation, 86.7% of patients with actual invasion of trachea and 85.7% of patients with actual invasion of other parts were in accordance with the esophageal activity examination results. Conclusion    Esophageal activity examination under X-ray fluoroscopy can accurately predict the resectability of upper thoracic esophageal cancer, which is a useful supplement to chest CT examination, especially in the aspect of judging the relationship between lesions and the trachea.

Background: () (2n = 2x = 16) is genus of flowering plants belonging to the Gelsemicaeae family. Method: Here, a high-quality genome assembly using the Oxford Nanopore Technologies (ONT) platform and high-throughput chromosome conformation capture techniques (Hi-C) were used. Results: A total of 56.11 Gb of raw GridION X5 platform ONT reads (6.23 Gb per cell) were generated. After filtering, 53.45 Gb of clean reads were obtained, giving 160 × coverage depth. The genome assemblies 335.13 Mb, close to the 338 Mb estimated by k-mer analysis, was generated with contig N50 of 10.23 Mb. The vast majority (99.2%) of the assembled sequence was anchored onto 8 pseudo-chromosomes. The genome completeness was then evaluated and 1338 of the 1440 conserved genes (92.9%) could be found in the assembly. Genome annotation revealed that 43.16% of the genome is composed of repetitive elements and 23.9% is composed of long terminal repeat elements. We predicted 26,768 protein-coding genes, of which 84.56% were functionally annotated. Conclusion The genomic sequences of could be a valuable source for comparative genomic analysis in the Gelsemicaeae family and will be useful for understanding the phylogenetic relationships of the indole alkaloid metabolism.

In case/control gene expression data, differential expression (DE) represents changes in gene expression levels across various biological conditions, whereas differential co-expression (DC) represents an alteration of correlation coefficients between gene pairs. Both DC and DE genes have been studied extensively in human diseases. However, effective approaches for integrating DC-DE analyses are lacking. Here, we report a novel analytical framework named DC&DEmodule for integrating DC and DE analyses and combining information from multiple case/control expression datasets to identify disease-related gene co-expression modules. This includes activated modules (gaining co-expression and up-regulated in disease) and dysfunctional modules (losing co-expression and down-regulated in disease). By applying this framework to microarray data associated with liver, gastric and colon cancer, we identified two, five and two activated modules and five, five and one dysfunctional module(s), respectively. Compared with the other methods, pathway enrichment analysis demonstrated the superior sensitivity of our method in detecting both known cancer-related pathways and those not previously reported. Moreover, we identified 17, 69, and 11 module hub genes that were activated in three cancers, which included 53 known and three novel cancer prognostic markers. Random forest classifiers trained by the hub genes showed an average of 93% accuracy in differentiating tumor and adjacent normal samples in the TCGA and GEO database. Comparison of the three cancers provided new insights into common and tissue-specific cancer mechanisms. A series of evaluations demonstrated the framework is capable of integrating the rapidly accumulated expression data and facilitating the discovery of dysregulated processes.
Gene Expression Profiling ; Gene Regulatory Networks ; Humans ; Microarray Analysis ; Neoplasms/genetics*