1b.Network_Reconstruction_files

In Network_Reconstruction_files.tgz are the major files required to run network reconstruction and some output files: - geneNamesTree # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions - Hs-Mm_EnsemblOrthology.txt # Ensembl orthology of Human and Mouse gene IDs - full_orthologs_map3c.txt # contains the published orthologs gene IDs for mapping used previously - list_k10 # list of k10 module numbers - list_species # list of species - OGIDS.txt # orthogroups - OGIDS.txt5 # processed orthogroups file - *_07.extrap.annotations.blast_out # extrapolation of motifs in cichlid gene promoters using human and mouse orthology - mz-speciesspecnames_clusterassign.txt # Arboretum module assignment of M. zebra genes - pn-speciesspecnames_clusterassign.txt # Arboretum module assignment of P. nyererei genes - ab-speciesspecnames_clusterassign.txt # Arboretum module assignment of A. burtoni genes - nb-speciesspecnames_clusterassign.txt # Arboretum module assignment of N. brichardi genes - on-speciesspecnames_clusterassign.txt # Arboretum module assignment of O. niloticus genes - geneNamesMapping.txt # gene orthology of cichlid IDs, Ensembl IDs and gene descriptions - MzPnAbNbOnGenome-BLAST_PresentNULLOGIDS-noCand-noTF.txt2 # 4209 orthogroups with NULL orthogroup IDs for one or species are actually present in the genome (mis-annotations etc.) and not lost/absent - motifenr_merged-TFBSs_map2d.txt # output of processing files in TFBSs - Motif Discovery in gene promoter regions - tftgco_merged.txt # output of processing TF-TG co-expression files

Network_Reconstruction_files.tgz 内收录了开展网络重构所需的主要文件与部分输出结果文件：
- geneNamesTree：记录慈鲷基因ID、Ensembl ID与基因描述信息的基因直系同源文件
- Hs-Mm_EnsemblOrthology.txt：人类与小鼠基因ID的Ensembl直系同源映射文件
- full_orthologs_map3c.txt：既往研究中用于序列映射的已发表直系同源基因ID集合
- list_k10：k10模块编号列表
- list_species：物种名录
- OGIDS.txt：直系同源组（orthogroups）文件
- OGIDS.txt5：经预处理的直系同源组文件
- *_07.extrap.annotations.blast_out：基于人类与小鼠直系同源关系，对慈鲷基因启动子区域基序进行外推预测得到的结果文件
- mz-speciesspecnames_clusterassign.txt：M. zebra基因的Arboretum模块分配结果文件
- pn-speciesspecnames_clusterassign.txt：P. nyererei基因的Arboretum模块分配结果文件
- ab-speciesspecnames_clusterassign.txt：A. burtoni基因的Arboretum模块分配结果文件
- nb-speciesspecnames_clusterassign.txt：N. brichardi基因的Arboretum模块分配结果文件
- on-speciesspecnames_clusterassign.txt：O. niloticus基因的Arboretum模块分配结果文件
- geneNamesMapping.txt：记录慈鲷基因ID、Ensembl ID与基因描述信息的基因直系同源文件
- MzPnAbNbOnGenome-BLAST_PresentNULLOGIDS-noCand-noTF.txt2：包含4209个直系同源组，其中部分物种的直系同源组ID为空（如注释错误等情况）但实际在基因组中存在而非丢失/缺失的文件
- motifenr_merged-TFBSs_map2d.txt：对转录因子结合位点（TFBSs）相关文件进行处理后的输出结果文件
- 基因启动子区域基序发现分析
- tftgco_merged.txt：对转录因子-靶基因共表达文件进行处理后的输出结果文件