Microarray analysis of transcripts with elevated expression in the rat medial or lateral habenula

Full article is available in "Brain Structure and Function":http://link.springer.com/article/10.1007/s00429-016-1195-zby Franziska Wagner, René Bernard, Christian Derst, Leon French and Rüdiger W. Veh.In vertebrates the “anti-reward-system” mainly is represented by the habenula and its medial (MHb) and especially lateral (LHb) complexes. So far, considerable knowledge has accumulated especially concerning subnuclear structures and the connectivities of MHb and LHb subnuclei. The present investigation aimed to obtain novel information, whether MHb or LHb or their subnuclei display characteristic gene products, which may shed more light on biological functions of these areas. Using microarray analysis of mRNAs expressed in microdissected habenular and thalamic control areas yielded expression values of 17,745 RNAs representing protein-coding genes, to which annotated gene names could be assigned. High relative values of genes with known expression in MHb, LHb or thalamus in the corresponding areas indicated a high precision of the microdissection procedure. <strong>File descriptions</strong> Supplemental Table 1: Expression matrix with gene symbols and normalized values for each ref-seq probe. Supplemental Table 2: The first 100 transcripts with the highest absolute expression in MHb and LHb.Supplemental Table 3: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.05 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.Supplemental Table 4: Transcripts with enhanced expression in the lateral habenula as compared to the thalamus (FDR &lt; 0.2 and fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 5: Genes deferentially expressed between medial and the lateral habenula (FDR &lt; 0.05 and absolute fold change &gt; 1.5). A “+” in column J or K indicates that this gene also is included in the indicated table and correspondingly depicted in the intersections of Figure 1. Gene ontology biological process terms are listed in the last column.<br>Supplemental Table 6: Gene ontology term enrichment results (six sheets in one table). These results were computed by ErmineJ. Gene Ontology files were downloaded on June 2015. Enrichment was tested on genes that had a corrected p &lt; 0.05 for each direction of change. Except for the LHb-Thal comparisons due to a limited number of genes that pass FDR &lt; 0.05. For these LHb-Thal comparisons the area under the receiver operating curve enrichment (AROC) method was applied.完整论文刊载于《Brain Structure and Function》期刊，链接为http://link.springer.com/article/10.1007/s00429-016-1195-z，作者为Franziska Wagner、René Bernard、Christian Derst、Leon French及Rüdiger W. Veh。在脊椎动物中，"抗奖赏系统（anti-reward-system）"主要由缰核（habenula）及其内侧缰核（MHb）、尤其是外侧缰核（LHb）复合体构成。迄今为止，学界已积累了大量关于内侧缰核与外侧缰核亚核结构及其连接特性的研究成果。本研究旨在探索全新科学问题：内侧缰核、外侧缰核及其亚核是否存在特异性基因表达产物，以期为阐明上述脑区的生物学功能提供新的线索。本研究通过对显微切割获取的缰核与丘脑对照区域的mRNA进行微阵列分析，共得到17745个编码蛋白质基因的RNA表达量数据，且均可匹配到已注释的基因名称。在对应脑区中，已知在内侧缰核、外侧缰核或丘脑表达的基因呈现较高相对表达量，这表明显微切割操作具有较高精准度。<strong>文件说明</strong> 补充表1：包含每个参考序列探针（ref-seq probe）的基因符号与标准化表达值的表达矩阵。 补充表2：在内侧缰核与外侧缰核中绝对表达量最高的前100个转录本。 补充表3：与丘脑相比，外侧缰核中表达上调的转录本（错误发现率（False Discovery Rate, FDR）< 0.05，折叠变化（fold change）> 1.5）。若J列或K列标注有"+"，则表明该基因同时包含于对应表格中，并在图1的交集区域中有所体现。最后一列列出了基因本体（Gene Ontology, GO）的生物学过程术语。 补充表4：与丘脑相比，外侧缰核中表达上调的转录本（错误发现率（False Discovery Rate, FDR）< 0.2，折叠变化（fold change）> 1.5）。若J列或K列标注有"+"，则表明该基因同时包含于对应表格中，并在图1的交集区域中有所体现。最后一列列出了基因本体（Gene Ontology, GO）的生物学过程术语。 补充表5：内侧缰核与外侧缰核之间差异表达的基因（错误发现率（False Discovery Rate, FDR）< 0.05，绝对折叠变化> 1.5）。若J列或K列标注有"+"，则表明该基因同时包含于对应表格中，并在图1的交集区域中有所体现。最后一列列出了基因本体（Gene Ontology, GO）的生物学过程术语。 补充表6：基因本体（Gene Ontology, GO）术语富集分析结果（单表内含6个工作表）。该分析结果由ErmineJ软件计算得到，基因本体文件下载于2015年6月。富集分析针对每个表达变化方向下校正后P值<0.05的基因进行；但外侧缰核-丘脑比较组除外，因满足错误发现率（False Discovery Rate, FDR）<0.05的基因数量有限，此类比较采用受试者工作特征曲线下面积（Area Under the Receiver Operating Characteristic curve, AROC）富集分析法。