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Table A.2: Filtered DNA-binding Protein Datasets
Table 1. Sequence-specific DNA-binding transcription factor GO categories
2005
"... In PAGE 5: ...Table1 (Sup- plementary Table 2 provides a comprehensive list, including categories we classified as expression related). It should be noted here that when we manually inspected proteins classified by GO as transcription factors, we found that the set also includes some basal (i.... ..."
Table A.1: SwissProt DNA-binding Protein Dataset
Table 1. Abbreviations of gene families. ad adhesion dn DNA binding and modiflcation an angiogenesis in invasion
Table 3, Most versatile superfamily combinations in multi- domain proteins Note, the combination with the greatest number of different functions is that of 1.95.1 and 7.33.1. Careful examination reveals that all the proteins with this combination are DNA-binding and most of them act as various hormone receptors. (In particular, HNF4_DROME and NR42_HUMAN also have transcription activator functions. Note that these two proteins are considerably longer than the others in this group and are not covered completely by structural matches: a large C-terminal and a large N-terminal portion are left uncovered respectively.)
2001
"... In PAGE 7: ... That is, the probability that two single-domain proteins that have the same superfamily structure have the same function (whether enzymatic or not) is about 2/3. Multi-domain proteins Table3 lists the combinations of superfamilies that have been associated with the greatest number of different functions in multi-domain proteins, with representative entries in Swiss-prot. The combination with the greatest number of different functions is that of 1.... ..."
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Table 1 Definition of positive and negative sets of matrix matches
2004
"... In PAGE 5: ... In the case of transcription factor binding sites this is particu- larly problematic, because DNA-binding proteins have over- lapping specificity, and we may therefore observe conservation of a binding site because it is bound by another factor with similar specificity. After evaluating all factors with binding specificity in Saccharomyces cerevisiae Promoter Database (SCPD) [33], we focus on Gal4p and Rpn4p for fur- ther analysis (see Table1 for properties of these factors, and Materials and methods for a description of the selection of positive and negative sets). The effects of evolutionary models on the discrimination of functional binding sites To evaluate the performance of our evolutionary method in correctly identifying bona fide binding sites, we calculated the p-values of the positive and negative sites for each factor, using MONKEY on alignments of all five genomes for Rpn4p and four species (with S.... ..."
Table 1 Gene ontology (GO) terms applied to 76 songbird cDNAs. GO terms form three large categories: molecular function, biological process, and cellular component. Individual cDNA products can have multiple functions and at least one cellular lo- cation, and thus, each cDNA is often assigned more than one term. For example, the 7 DNA binding proteins are a subset of the 16 songbird clones with presumed locations in the nucleus
"... In PAGE 8: ... Of all the 207 Genbank matched clones, 76 (37%) were found in the GO database, which we annotated with GO terms. A list of the most frequent annotated terms is in Table1 . Most represent nucleus, cell mem- brane, and signal transduction proteins.... ..."
Table 1. Regulatory proteins exhibiting sequence similarity to S. typhimurium SprB.
"... In PAGE 2: ...HTH) family signature (Fuqua et al., 1996) (Fig. 2B). A summary of these homologies is shown in Table1 . The DNA-binding motif is located in the C-terminal end of these proteins, which can be grouped in two different sub- classes based on the mechanism by which they are acti- vated.... ..."
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