A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions

Endometriosis is a common inflammatory
estrogen-dependent gynecological disorder, associated with pelvic pain and
reduced fertility in women. Several aspects of this disorder and its cellular
and molecular etiology remain unresolved. We have analyzed the global gene
expression patterns in the endometrium, peritoneum and in endometriosis lesions
of endometriosis patients and in the endometrium and peritoneum of healthy women.
In this report, we present the EndometDB, an interactive web-based user
interface for browsing the gene expression database of collected samples
without the need for computational skills. The current database incorporates
the expression data from 115 patients and 53 controls, with over 24000 genes
and clinical features, such as their age, disease stages, hormonal medication,
menstrual cycle phase, and the different endometriosis lesion types. Using the
web-tool, the end-user can easily generate various plot outputs, including
boxplots, heatmaps and scatterplots, and the generated plot outputs can be downloaded
in pdf-format. Availability
and implementation: The web-based user interface is implemented using HTML5,
JavaScript, CSS, Plotly and R. It is freely available from URL: https://endometdb.utu.fi/gene_analysis.<br>Endomet Database dump and schema.<br><br>Number of samples used in quantitative real-time PCR.<br><br>Pie chart showing the percentage of the different types of samples analyzed for global gene expression by microarrays.<br>Multidimensional scaling of WNT pathway genes of
the endometrium vs endometriosis samples using Canberra distance metric and
colored by tissues.<b> </b>The analysis separates endometrial specimens from
the different lesions<b>.</b><b><br></b>Result of scree test for PCA analysis of WNT
pathway genes. The scree plot explains how much the principal components
account for the total variance in the expression data.<b><br></b>

子宫内膜异位症（Endometriosis）是一类常见的炎症性雌激素依赖性妇科疾病，与女性盆腔疼痛及生育能力降低密切相关。目前该疾病的诸多层面，及其细胞与分子病因学机制仍未明确。本研究分析了子宫内膜异位症患者的子宫内膜、腹膜及异位病灶，以及健康女性的子宫内膜与腹膜组织中的全局基因表达谱。
本研究构建了EndometDB数据库，这是一款交互式网页用户界面，无需专业计算技能即可浏览所收录样本的基因表达数据库。当前数据库整合了115例患者与53例健康对照的表达数据，涵盖超过24000个基因及多项临床特征，包括受试者年龄、疾病分期、激素用药情况、月经周期阶段，以及不同类型的子宫内膜异位症病灶。通过该网页工具，终端用户可便捷生成多种可视化绘图结果，包括箱线图（boxplots）、热图（heatmaps）与散点图（scatterplots），且生成的绘图文件可导出为PDF格式。
可用性与实现：该网页用户界面基于HTML5、JavaScript、CSS、Plotly及R语言开发，可通过以下网址免费访问：https://endometdb.utu.fi/gene_analysis。
子宫内膜异位症数据库备份文件与架构信息。
定量实时PCR（quantitative real-time PCR）所用样本数量。
展示通过微阵列（microarrays）分析全局基因表达的各类样本占比的饼图。
基于堪贝拉距离（Canberra distance）度量的WNT通路基因多维缩放分析：将子宫内膜样本与子宫内膜异位症病灶样本按组织类型着色，该分析可有效区分不同病灶来源的子宫内膜标本。
WNT通路基因主成分分析（PCA）的碎石检验结果。碎石图可展示各主成分对表达数据总方差的解释程度。