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Phylum-level taxonomic units were used as taxon identifiers (supplementary table S1, Supplementary Material online).
For interpretation of whole genome ChIP-chip datasets in the K562 cell line in the context of gene expression, data was considered for only those genes consistently called either absent or present by MAS5 on Affymetrix Expression GeneChips and which also had ENSEMBL identifiers (Supplementary Table S9).
Because EMAP ontologies were recently updated to the EMAPA ontology (34), we mapped the presented brain regions also to these identifiers (Supplementary Table S1).
This additional information allows to search with up to 18 different identifiers (Supplementary Material S1) for cross-references depending on the organism.
To analyse selected genes in human breast cancer microarray data (Wang et al, 2005), spots were linked to Affymetrix probe sets using Entrez Gene and Ensemble identifiers (Supplementary Table S2).
The first step of the Metascape analysis workflow is gene identifier conversion (Supplementary Figure 2).
The full set of KLF/SPs identified in this study with their corresponding accession numbers or protein/transcript identifiers are available in supplementary table S1, Supplementary Material online.
The sequence contexts of each of the reported polymorphisms, as well as their "rs" identifiers, are provided in Supplementary Table S2, while the corresponding reconstructed haplotypes (see Materials and Methods) are listed in Supplementary Table S3.
Detailed sample and run identifiers are listed in Supplementary Table S11.
The full list of sequences used for the tree and their database identifiers are given as supplementary material [see Additional file 1].
The tables included in this manuscript and supplementary spreadsheets include the analogous GeneDB identifiers and hyperlinks to the appropriate data pages for each sequence.
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