Analysis of temporal lens gene expression microarrays to expand the eye gene discovery tool iSyTE

Purpose: While the bioinformatics gene-discovery tool iSyTE (integrated Systems Tool for Eye gene discovery) has proved effective in identifying new cataract-linked genes, it primarily depended on lens-enriched expression of just three wild-type mouse embryonic stages. To increase iSyTE's efficacy, a broad range of embryonic (E) and postnatal (P) lens microarray datasets from wild-type and specific gene-perturbation mutant mice were analyzed and a new web-interface was developed for their effective access and downstream-analysis. Methods: Five new mouse lens microarrays were generated and analyzed with all publicly available Affymetrix and Illumina lens datasets representing the stages E9.5, E10.25, E10.5, E11.5, E12.5, E15.5, E16.5, E17.5, E19.5, P0, P2, P4, P8, P12, P20, P28, P30, P42, P52, P56, P60 and mouse mutants for the genes: Brg1, CBP:p300, E2f1:E2f2:E2f3, Foxe3, Hsf4, Klf4, Mafg:Mafk, Notch2, Pax6, Sparc, Tdrd7. Results: The integrated lens microarray analysis accurately reflects established gene expression patterns and defines a new lens-signature gene-set for embryonic and postnatal stages that includes several novel candidates namely, Grifin, Ogn, Fabp5, Mboat1, Tmem40, Dhx32, Aldoc, Pgam2, Hmgn3, Mocs2, Gprc5b, Gstm1, Npl, and Zbtb8b. Combined analyses of 32 developmental/genetic data-conditions identifies several new transcription and signaling factors that potentially function in lens development and/or homeostasis. Conclusions: The updated iSyTE web-interface: (1) comprehensively informs on normal lens developmental and cataract-associated transcriptome dynamics and identifies new high-priority candidates for these processes, and (2) offers user-friendly visualization. Microarray comparison of lenses from multiple embryonic and postnatal stages vs. embryonic whole body control and mutant vs. control. This dataset includes lens samples from multiple postnatal stages, and embryonic whole body (minus eye) controls.研究目的：生物信息学基因发现工具iSyTE（integrated Systems Tool for Eye gene discovery）已被证实可有效识别新的白内障相关基因，但其仅依赖于三个野生型小鼠胚胎阶段的晶状体富集表达数据，存在应用局限。为提升iSyTE的效能，本研究分析了涵盖野生型及特定基因扰动突变小鼠的多套胚胎期（E）与出生后（P）晶状体微阵列数据集，并开发了全新的Web界面以实现这些数据的高效访问与下游分析。 研究方法：本研究新生成并分析了5套小鼠晶状体微阵列数据，同时整合了所有公开可用的Affymetrix及Illumina平台晶状体数据集，覆盖的发育阶段包括E9.5、E10.25、E10.5、E11.5、E12.5、E15.5、E16.5、E17.5、E19.5、P0、P2、P4、P8、P12、P20、P28、P30、P42、P52、P56、P60，以及携带Brg1、CBP:p300、E2f1:E2f2:E2f3、Foxe3、Hsf4、Klf4、Mafg:Mafk、Notch2、Pax6、Sparc、Tdrd7基因突变的小鼠模型数据。 研究结果：整合后的晶状体微阵列分析准确复现了已证实的基因表达模式，并定义了一套适用于胚胎期与出生后阶段的全新晶状体特征基因集，其中包含Grifin、Ogn、Fabp5、Mboat1、Tmem40、Dhx32、Aldoc、Pgam2、Hmgn3、Mocs2、Gprc5b、Gstm1、Npl及Zbtb8b等多个新型候选基因。通过对32个发育/遗传数据条件的联合分析，本研究鉴定出若干可能参与晶状体发育和/或稳态调控的新型转录因子与信号因子。 研究结论：更新后的iSyTE Web界面具备两大核心功能：（1）全面呈现正常晶状体发育及白内障相关的转录组动态变化特征，并为上述过程筛选出高优先级的新型候选基因；（2）提供友好易用的可视化功能。本研究实现了多胚胎期、多出生后期晶状体样本与胚胎全身（剔除眼部）对照样本，以及突变体与对照样本的微阵列比较分析。本次数据集包含多出生后期晶状体样本及胚胎全身（不含眼部）对照样本。