Additional file 2 of Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response

Additional file 2: Table 01. List of 2,893 differentially expressed genes identified in whole root data. Table 02. List of 2,739 differentially expressed genes identified using epidermis specific RNA-seq data with controls at all time points. Fields included are AGI, Alias(es), Cluster number, and a flag indicating whether the gene was differentially expressed at 6, 12, 18, 24, 30 or 36 hours. Table 03. List of 337 motifs identified using AME (65) with the DAP-seq (66) database. Table 04. List of 29 Consistent transcription factors identified in 20 runs of logistic regression with LASSO. Name, AGI and GO terms identified on arabidopsis.org (TAIR) are provided. Table 05. List of putative targets associated with each of the 29 consistent transcription factors. List includes the name of transcription factor, AGI of target, flag indicating whether target is 1) a known iron gene and/or 2) a transcription factor. Table 06. GO terms enriched in the group of targets associated with each of 29 consistent transcription factors. Table 07. Subset of GO terms from Supplementary Table 03 that include reference to "iron". GO ID, GO term, adjusted p-value and transcription factor name or AGI provided. Table 08. Subset of GO terms from Supplementary Table 03 that include reference to "root". GO ID, GO term, adjusted p-value and transcription factor name or AGI provided. Table 09. Subset of GO terms from Supplementary Table 03 that include reference to "epidermis". GO ID, GO term, adjusted p-value and transcription factor name or AGI provided.

附加文件2：表01。从全根组织转录组数据中鉴定得到的2893个差异表达基因(differentially expressed genes)列表。表02。基于表皮特异性RNA-seq数据，并纳入全时间点对照样本，筛选得到的2739个差异表达基因列表。该表格包含以下字段：AGI、别名(Alias(es))、聚类编号，以及用于标记该基因是否在6、12、18、24、30或36小时时发生差异表达的标识。表03。使用AME(65)结合DAP-seq(66)数据库鉴定得到的337个基序(motif)列表。表04。经20次带LASSO惩罚的逻辑回归分析筛选得到的29个稳定转录因子列表。表格提供了这些转录因子的名称、AGI以及从arabidopsis.org(TAIR)获取的基因本体(GO, Gene Ontology)术语。表05。与上述29个稳定转录因子各自相关的潜在靶基因列表。该列表包含转录因子名称、靶基因的AGI，以及用于标记靶基因是否为1）已知铁代谢相关基因和/或2）转录因子的标识。表06。与29个稳定转录因子各自相关的靶基因集合中富集的基因本体(GO)术语。表07。从补充表03中提取的包含“铁”相关描述的GO术语子集。表格包含GO ID、GO术语、校正P值(adjusted p-value)，以及对应转录因子名称或AGI。表08。从补充表03中提取的包含“根”相关描述的GO术语子集。表格包含GO ID、GO术语、校正P值，以及对应转录因子名称或AGI。表09。从补充表03中提取的包含“表皮”相关描述的GO术语子集。表格包含GO ID、GO术语、校正P值，以及对应转录因子名称或AGI。