Vertebrate motif clusters 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（cis-bp）的脊椎动物基序（motif）簇
当前版本：3.0
所有基序信息均基于Weirauch等人2014年发表的cis-bp数据库（http://dx.doi.org/10.1016/j.cell.2014.08.009）。
基序信息下载自cis-bp数据库（http://cisbp.ccbr.utoronto.ca/；2014年10月检索获取）。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）、暗纹多纪鲀（Tetraodon nigroviridis）、非洲爪蟾（Xenopus laevis）、热带爪蟾（Xenopus tropicalis）、家鸡（Gallus gallus）、火鸡（Meleagris gallopavo）、卡罗莱纳安乐蜥（Anolis carolinensis）、灰短尾负鼠（Monodelphis domestica）、红鳍东方鲀（Takifugu rubripes）、王鲑（Oncorhynchus tshawytscha）、三刺棘鱼（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存在直接结合证据的基序。
在cis-bp数据库注释的每个基序家族范围内，所有基序均采用GimmeMotifs工具包（GimmeMotifs）的`gimme cluster`命令完成聚类，聚类阈值设置为0.9999（Heeringen与Veenstra，2011）[http://github.com/simonvh/gimmemotifs]。聚类后的基序名称会标注其所属的基序家族名称；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命名。
基序与结合因子的双向注释（即基序对应因子、因子对应基序）基于cis-bp注释中智人、小家鼠及热带爪蟾的蛋白质注释，涵盖直接结合基序与推定基序。本数据集为上述三个物种的整合数据，可能存在信息不全的情况。如需获取更多物种特异性注释，请参阅可从cis-bp数据库获取的「TF_Information_all_motifs.txt」文件。