Vertebrate motif cluster v3.0

# Vertebrate motif clusters from cis-bp Current version: 3.0 All the motif information is based on the cis-bp database described in (Weirauch et al., 2014)[http://dx.doi.org/10.1016/j.cell.2014.08.009]. Motif information was downloaded from cis-bp (http://cisbp.ccbr.utoront/o.ca/; retrieved Oct 2014). Vertebrate motifs were selected based on the following list of species: Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Tetraodon nigroviridis, Xenopus laevis, Xenopus tropicalis, Gallus gallus, Meleagris gallopavo, Anolis carolinensis, Monodelphis domestica, Takifugu rubripes, Oncorhynchus tshawytscha, Gasterosteus aculeatus, Ornithorhynchus anatinus, Sus scrofa, Cavia porcellus, Oryctolagus cuniculus, Pan troglodytes, Taeniopygia guttata. Only motifs with direct evidence of binding in any of these species were selected. Within every motif family, as annotated by cis-bp, all motifs were clustered using 'gimme cluster' from the GimmeMotifs package (Heeringen and Veenstra, 2011)[http://github.com/simonvh/gimmemotifs] with a threshold of 0.9999. The cluster motif names are annotated with the motif family name. Any name containing 'Average' is a unique yet arbitrary name of a specific cluster of motifs. The annotation of motifs to factors and vice versa is based on the annotation of human, mouse and Xenopus tropicalis proteins from the cis-bp annotation and includes direct as well as inferred motifs. This is an aggregate over these three species, and might be incomplete. For more (species-)specific annotation, see the file 'TF_Information_all_motifs.txt' that can be obtained from cis-bp.

# 来自cis-bp数据库的脊椎动物基序（motif）簇 当前版本：3.0
所有基序（motif）信息均基于Weirauch等人2014年发表的cis-bp数据库[http://dx.doi.org/10.1016/j.cell.2014.08.009]。基序（motif）数据下载自cis-bp数据库（http://cisbp.ccbr.utoront/o.ca/; retrieved Oct 2014）。本次数据集选取的脊椎动物基序对应以下物种：智人（Homo sapiens）、小家鼠（Mus musculus）、褐家鼠（Rattus norvegicus）、斑马鱼（Danio rerio）、青斑四齿鲀（Tetraodon nigroviridis）、非洲爪蟾（Xenopus laevis）、热带爪蟾（Xenopus tropicalis）、原鸡（Gallus gallus）、火鸡（Meleagris gallopavo）、安乐蜥（Anolis carolinensis）、灰短尾负鼠（Monodelphis domestica）、红鳍东方鲀（Takifugu rubripes）、大鳞大麻哈鱼（Oncorhynchus tshawytscha）、三刺鱼（Gasterosteus aculeatus）、鸭嘴兽（Ornithorhynchus anatinus）、野猪（Sus scrofa）、豚鼠（Cavia porcellus）、穴兔（Oryctolagus cuniculus）、黑猩猩（Pan troglodytes）、斑胸草雀（Taeniopygia guttata）。仅选取在上述任一物种中具有直接结合证据的基序。在cis-bp数据库注释的每个基序家族内，所有基序均使用GimmeMotifs工具包（Heeringen与Veenstra，2011）[http://github.com/simonvh/gimmemotifs]中的`gimme cluster`命令进行聚类，聚类阈值设为0.9999。聚类后的基序名称以其所属的基序家族名称进行注释。所有包含'Average'字样的名称，均为对应特定基序簇的唯一且自定义名称。基序与转录因子的注释关联（及反向关联）基于cis-bp数据库中对人、小鼠及热带爪蟾蛋白质的注释，涵盖直接结合基序与推断得到的基序。本数据集为这三个物种的聚合数据，可能存在不完整性。如需获取物种特异性更强的注释信息，请参阅可从cis-bp数据库下载的文件`TF_Information_all_motifs.txt`。