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Relevant bibliographies by topics / DNA binding protein; Yeast/CPF1

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Academic literature on the topic 'DNA binding protein; Yeast/CPF1'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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Journal articles on the topic "DNA binding protein; Yeast/CPF1"

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Dorsman, J. C., A. Gozdzicka-Jozefiak, W. C. Van Heeswijk, and L. A. Grivell. "Multi-functional DNA proteins in yeast: The factors GFI and GFII are identical to the ARS-binding factor ABFI and the centromere-binding factor CPF1 respectively." Yeast 7, no. 4 (May 1991): 401–12. http://dx.doi.org/10.1002/yea.320070410.

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Lane, Shelley, Song Zhou, Ting Pan, Qian Dai, and Haoping Liu. "The Basic Helix-Loop-Helix Transcription Factor Cph2 Regulates Hyphal Development in CandidaalbicansPartly via Tec1." Molecular and Cellular Biology 21, no. 19 (October 1, 2001): 6418–28. http://dx.doi.org/10.1128/mcb.21.19.6418-6428.2001.

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ABSTRACT Candida albicans undergoes a morphogenetic switch from budding yeast to hyphal growth form in response to a variety of stimuli and growth conditions. Multiple signaling pathways, including a Cph1-mediated mitogen-activated protein kinase pathway and an Efg1-mediated cyclic AMP/protein kinase A pathway, regulate the transition. Here we report the identification of a basic helix-loop-helix transcription factor of the Myc subfamily (Cph2) by its ability to promote pseudohyphal growth inSaccharomyces cerevisiae. Like sterol response element binding protein 1, Cph2 has a Tyr instead of a conserved Arg in the basic DNA binding region. Cph2 regulates hyphal development in C. albicans, ascph2/cph2 mutant strains show medium-specific impairment in hyphal development and in the induction of hypha-specific genes. However, many hypha-specific genes do not have potential Cph2 binding sites in their upstream regions. Interestingly, upstream sequences of all known hypha-specific genes are found to contain potential binding sites for Tec1, a regulator of hyphal development. Northern analysis shows that TEC1 transcription is highest in the medium in which cph2/cph2 displays a defect in hyphal development, and Cph2 is necessary for this transcriptional induction of TEC1. In vitro gel mobility shift experiments show that Cph2 directly binds to the two sterol regulatory element 1-like elements upstream of TEC1. Furthermore, the ectopic expression of TEC1 suppresses the defect ofcph2/cph2 in hyphal development. Therefore, the function of Cph2 in hyphal transcription is mediated, in part, through Tec1. We further show that this function of Cph2 is independent of the Cph1- and Efg1-mediated pathways.

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Niedenthal, Rainer K., Mark Sen-Gupta, Wilmen Andreas, and Johannes H. Hegemann. "Cpf1 protein induced bending of yeast centromere DNA element I." Nucleic Acids Research 21, no. 20 (1993): 4726–33. http://dx.doi.org/10.1093/nar/21.20.4726.

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Niedenthal, R., R. Stoll, and J. H. Hegemann. "In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1." Molecular and Cellular Biology 11, no. 7 (July 1991): 3545–53. http://dx.doi.org/10.1128/mcb.11.7.3545.

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The centromere DNA element I (CDEI) is an important component of Saccharomyces cerevisiae centromere DNA and carries the palindromic sequence CACRTG (R = purine) as a characteristic feature. In vivo, CDEI is bound by the helix-loop-helix protein CPF1. This article describes the in vivo analysis of all single-base-pair substitutions in CDEI in the centromere of an artificial chromosome and demonstrates the importance of the palindromic sequence for faithful chromosome segregation, supporting the notion that CPF1 binds as a dimer to this binding site. Mutational analysis of two conserved base pairs on the left and two nonconserved base pairs on the right of the CDEI palindrome revealed that these are also relevant for mitotic CEN function. Symmetrical mutations in either half-site of the palindrome affect centromere activity to a different extent, indicating nonidentical sequence requirements for binding by the CPF1 homodimer. Analysis of double point mutations in CDEI and in CDEIII, an additional centromere element, indicate synergistic effects between the DNA-protein complexes at these sites.

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Niedenthal, R., R. Stoll, and J. H. Hegemann. "In vivo characterization of the Saccharomyces cerevisiae centromere DNA element I, a binding site for the helix-loop-helix protein CPF1." Molecular and Cellular Biology 11, no. 7 (July 1991): 3545–53. http://dx.doi.org/10.1128/mcb.11.7.3545-3553.1991.

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The centromere DNA element I (CDEI) is an important component of Saccharomyces cerevisiae centromere DNA and carries the palindromic sequence CACRTG (R = purine) as a characteristic feature. In vivo, CDEI is bound by the helix-loop-helix protein CPF1. This article describes the in vivo analysis of all single-base-pair substitutions in CDEI in the centromere of an artificial chromosome and demonstrates the importance of the palindromic sequence for faithful chromosome segregation, supporting the notion that CPF1 binds as a dimer to this binding site. Mutational analysis of two conserved base pairs on the left and two nonconserved base pairs on the right of the CDEI palindrome revealed that these are also relevant for mitotic CEN function. Symmetrical mutations in either half-site of the palindrome affect centromere activity to a different extent, indicating nonidentical sequence requirements for binding by the CPF1 homodimer. Analysis of double point mutations in CDEI and in CDEIII, an additional centromere element, indicate synergistic effects between the DNA-protein complexes at these sites.

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Meluh, P. B., and D. Koshland. "Evidence that the MIF2 gene of Saccharomyces cerevisiae encodes a centromere protein with homology to the mammalian centromere protein CENP-C." Molecular Biology of the Cell 6, no. 7 (July 1995): 793–807. http://dx.doi.org/10.1091/mbc.6.7.793.

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The MIF2 gene of Saccharomyces cerevisiae has been implicated in mitosis. Here we provide genetic evidence that MIF2 encodes a centromere protein. Specifically, we found that mutations in MIF2 stabilize dicentric minichromosomes and confer high instability (i.e., a synthetic acentric phenotype) to chromosomes that bear a cis-acting mutation in element I of the yeast centromeric DNA (CDEI). Similarly, we observed synthetic phenotypes between mutations in MIF2 and trans-acting mutations in three known yeast centromere protein genes-CEP1/CBF1/CPF1, NDC10/CBF2, and CEP3/CBF3B. In addition, the mif2 temperature-sensitive phenotype can be partially rescued by increased dosage of CEP1. Synthetic lethal interactions between a cep1 null mutation and mutations in either NDC10 or CEP3 were also detected. Taken together, these data suggest that the Mif2 protein interacts with Cep1p at the centromere and that the yeast centromere indeed exists as a higher order protein-DNA complex. The Mif2 and Cep1 proteins contain motifs of known transcription factors, suggesting that assembly of the yeast centromere is analogous to that of eukaryotic enhancers and origins of replication. We also show that the predicted Mif2 protein shares two short regions of homology with the mammalian centromere Ag CENP-C and that two temperature-sensitive mutations in MIF2 lie within these regions. These results provide evidence for structural conservation between yeast and mammalian centromeres.

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Mellor, J., J. Rathjen, W. Jiang, and S. J. Dowell. "DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine prototrophy in yeast." Nucleic Acids Research 19, no. 11 (1991): 2961–69. http://dx.doi.org/10.1093/nar/19.11.2961.

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Mellor, J., J. Rathjen, W. Jiang, C. A. Barnes, and S. J. Dowell. "DNA binding of CPF1 is required for optimal centromere function but not for maintaining methionine phototrophy in yeast." Nucleic Acids Research 19, no. 18 (1991): 5112. http://dx.doi.org/10.1093/nar/19.18.5112.

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Morrow, B. E., Q. Ju, and J. R. Warner. "A bipartite DNA-binding domain in yeast Reb1p." Molecular and Cellular Biology 13, no. 2 (February 1993): 1173–82. http://dx.doi.org/10.1128/mcb.13.2.1173.

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The REB1 gene encodes a DNA-binding protein (Reb1p) that is essential for growth of the yeast Saccharomyces cerevisiae. Reb1p binds to sites within transcriptional control regions of genes transcribed by either RNA polymerase I or RNA polymerase II. The sequence of REB1 predicts a protein of 809 amino acids. To define the DNA-binding domain of Reb1p, a series of 5' and 3' deletions within the coding region was constructed in a bacterial expression vector. Analysis of the truncated Reb1p proteins revealed that nearly 400 amino acids of the C-terminal portion of the protein are required for maximal DNA-binding activity. To further define the important structural features of Reb1p, the REB1 homolog from a related yeast, Kluyveromyces lactis, was cloned by genetic complementation. The K. lactis REB1 gene supports active growth of an S. cerevisiae strain whose REB1 gene has been deleted. The Reb1p proteins of the two organisms generate almost identical footprints on DNA, yet the K. lactis REB1 gene encodes a polypeptide of only 595 amino acids. Comparison of the two Reb1p sequences revealed that within the region necessary for the binding of Reb1p to DNA were two long regions of nearly perfect identity, separated in the S. cerevisiae Reb1p by nearly 150 amino acids but in the K. lactis Reb1p by only 40 amino acids. The first includes a 105-amino-acid region related to the DNA-binding domain of the myb oncoprotein; the second bears a faint resemblance to myb. The hypothesis that the DNA-binding domain of Reb1p is formed from these two conserved regions was confirmed by deletion of as many as 90 amino acids between them, with little effect on the DNA-binding ability of the resultant protein. We suggest that the DNA-binding domain of Reb1p is made up of two myb-like regions that, unlike myb itself, are separated by as many as 150 amino acids. Since Reb1p protects only 15 to 20 nucleotides in a chemical or enzymatic footprint assay, the protein must fold such that the two components of the binding site are adjacent.

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Morrow, B. E., Q. Ju, and J. R. Warner. "A bipartite DNA-binding domain in yeast Reb1p." Molecular and Cellular Biology 13, no. 2 (February 1993): 1173–82. http://dx.doi.org/10.1128/mcb.13.2.1173-1182.1993.

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The REB1 gene encodes a DNA-binding protein (Reb1p) that is essential for growth of the yeast Saccharomyces cerevisiae. Reb1p binds to sites within transcriptional control regions of genes transcribed by either RNA polymerase I or RNA polymerase II. The sequence of REB1 predicts a protein of 809 amino acids. To define the DNA-binding domain of Reb1p, a series of 5' and 3' deletions within the coding region was constructed in a bacterial expression vector. Analysis of the truncated Reb1p proteins revealed that nearly 400 amino acids of the C-terminal portion of the protein are required for maximal DNA-binding activity. To further define the important structural features of Reb1p, the REB1 homolog from a related yeast, Kluyveromyces lactis, was cloned by genetic complementation. The K. lactis REB1 gene supports active growth of an S. cerevisiae strain whose REB1 gene has been deleted. The Reb1p proteins of the two organisms generate almost identical footprints on DNA, yet the K. lactis REB1 gene encodes a polypeptide of only 595 amino acids. Comparison of the two Reb1p sequences revealed that within the region necessary for the binding of Reb1p to DNA were two long regions of nearly perfect identity, separated in the S. cerevisiae Reb1p by nearly 150 amino acids but in the K. lactis Reb1p by only 40 amino acids. The first includes a 105-amino-acid region related to the DNA-binding domain of the myb oncoprotein; the second bears a faint resemblance to myb. The hypothesis that the DNA-binding domain of Reb1p is formed from these two conserved regions was confirmed by deletion of as many as 90 amino acids between them, with little effect on the DNA-binding ability of the resultant protein. We suggest that the DNA-binding domain of Reb1p is made up of two myb-like regions that, unlike myb itself, are separated by as many as 150 amino acids. Since Reb1p protects only 15 to 20 nucleotides in a chemical or enzymatic footprint assay, the protein must fold such that the two components of the binding site are adjacent.

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Dissertations / Theses on the topic "DNA binding protein; Yeast/CPF1"

1

Kent, Nicholas A. "Chromatin modulation in Saccharomyces cerevisiae by Centromere and Promoter Factor 1." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.359458.

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2

Luo, Dan. "Novel crosslinking technologies to assess protein-DNA binding and DNA-DNA complexes for gene delivery and expression." The Ohio State University, 1997. http://rave.ohiolink.edu/etdc/view?acc_num=osu1114436532.

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Zhong, Shan. "Studies on the human homolog of the yeast Noc3p in human cells /." View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?BICH%202004%20ZHONG.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004.
Includes bibliographical references (leaves 83-100). Also available in electronic version. Access restricted to campus users.

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Hu, Yun. "Study of the yeast Noc3p homolog in human cells /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20HU.

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TIMMERMAN, JOHANNA. "Preparation and structural study of the dna-binding domain of the cyp1 protein of the yeast saccharomyces cerevisiae." Paris 11, 1994. http://www.theses.fr/1994PA112429.

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Dans la levure saccharomyces cerevisiae, la proteine cyp1 est un regulateur de la transcription de nombreux genes dont l'expression est dependante de l'oxygene. Nous nous sommes interesse a la determination de la structure tridimensionnelle du domaine de fixation a l'adn de cette proteine. Cette partie contient un motif cys-xaa(2)-cys-xaa(6)-cys-xaa(6)-cys-xaa(2)-cys-xaa(8)-cys, que l'on retrouve dans de nombreuses proteines de levure interagissant avec l'adn, en particulier dans la proteine gal4. Le but a long terme est de determiner le complexe cyp1-adn par resonance magnetique nucleaire. Dans ce travail nous presentons le clonage et l'expression dans escherichia coli des quatre fragments differents correspondant a la partie n-terminale de l'activateur cyp1 responsable de la fixation a l'adn. Le fragment cyp1(49-126) a ete choisi pour une etude structurale par resonance magnetique nucleaire. Pour ce fragment, un protocole de purification a ete mis au point. Nous montrons ensuite que le zinc est un element essentiel de la structure de la proteine et que le fragment cyp1(49-126) possede 2 atomes de zinc. Les memes resultats ont ete observes lorsqu'on substitue deux atomes de zinc par les atomes cadmium 113. Par resonance magnetique nucleaire, nous avons demontre que les six cysteines du motif ligandent les deux atomes de cadmium. Le fragment a ete ensuite marque avec de l'azote 15. L'ensemble des experiences rmn homonucleaires a deux dimensions (cosy, tocsy et noesy) et heteronucleaires a deux et trois dimensions (hmqc, noe-hmqc, hohaha-hmqc) a permis l'attribution de la partie n-terminale de cyp1(49-126). Les donnees experimentales obtenues par ces experiences ont ete utilisees dans des programmes de modelisation, diana et x-plor. Une structure tridimensionnelle du fragment a pu etre presentee et montre que notre fragment est replie en cluster a zinc

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Jolly, Emmitt R. Jr. "Identification of meiotic regulatory targets of Ndt80 by biochemical and genetic analysis /." 2004. http://wwwlib.umi.com/dissertations/fullcit/3136058.

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Omar, Syed A. A. "Characterizing Protein-Protein Interactions of B0238.11, a Previously Uncharacterized Caenorhabditis elegans Intergenic Spacer Binding Protein." Thesis, 2012. http://hdl.handle.net/10214/3619.

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A protein, B0238.11, was identified in a yeast one-hybrid screen to bind to the ribosomal intergenic spacer region (IGS) of Caenorhabditis elegans. Proteins interacting with this region of the DNA have been implicated in ribosome biogenesis in other model organisms, so it is also possible that B0238.11 plays a role in RNA transcription by interacting with RNA polymerase I or other transcription machinery. Thus, the goal of this study was to further characterize the structure and function of B0238.11. I used yeast two-hybrid experiments to identify proteins that interact with B0238.11 within the nucleus. RPS-0, K04G2.2, DPY-4, EFT-3, PAL-1, and B0238.11, itself, were found to bind to B0238.11. Additionally, I analysed the amino acid sequence of B0238.11 using in silico bioinformatics methods to determine its structure and putative function and also to identify and characterize the other interacting proteins. I found that B0238.11 contains a high-mobility group box domain, which is also found in HMO1P in yeast and UBF in vertebrates. These other proteins also bind to the IGS, are known to form homodimers and have been implicated in the initiation of ribosomal RNA transcription. Here I scrutinize the validity of the interaction between each protein and B0238.11. I conclude that B0238.11 is likely to be a C. elegans homolog of UBF and present an updated interactome map for B0238.11.
Synopsis: I carried out yeast two-hybrid assay to find proteins interacting with B0238.11 (O16487_CAEEL). I found that this protein's DNA-binding profile and protein interaction profile mimic other HMG-box containing proteins UBF and HMO1P which are involved in ribosomal RNA transcription initiation. Acknowledgements: I would like to thank my supervisor, Dr. Teresa J. Crease, for not only giving me the opportunity to investigate an interesting topic in Molecular Biology, but also for her patient guidance, encouragement and sound advice. I feel extremely lucky to have a supervisor who cared so much about my work, who responded to my questions and queries so promptly, and was always available to discuss project and career related matters. I would also like to thank Dr. Todd Gillis and Dr. Terry Van Raay for their careful consideration of this project and timely constructive criticisms that helped shape my project. I would like to thank all the members of my committee for helping me see things from different perspectives and helping me develop and critical and mature understanding of the scientific process. I must also express my gratitude to Dr. Robin Floyd for allowing me to build upon his work and Dr. Marian Walhout, at the University of Massachusetts, for providing the Caenorhabditis elegans complimentary DNA library. A large part of this project would not have been possible without the people at the genomics facility in the Department of Integrative Biology, I commend their professionalism and punctuality in delivering results. Completing this work would have been all the more difficult were it not for the support and friendship provided by my peers Shannon Eagle, Tyler Elliott, Nick Jeffery, Joao Lima, Sabina Stanescu, Fatima Mitterboeck and Paola Pierossi. And finally, I would like to thank my parents and siblings Sara Omar and Ali Omar for their continued support through good times and bad, and letting me use their laptops when mine broke down.

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Tripathi, Pankaj. "Selective Binding Of Meiosis-Specific Yeast Hop1 Protein, or Its ZnF Motif, To The Holliday Junction Distorts The DNA Structure : Implications For Junction Migration And Resolution." Thesis, 2008. http://hdl.handle.net/2005/894.

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Saccharomyces cerevisiae HOP1, which encodes a component of the synaptonemal complex, plays an important role in both gene conversion and crossing over between homologs, as well as enforces the meiotic recombination checkpoint control over the progression of recombination intermediates. The zinc-finger motif (Znf) 348CX2CX19CX2C374) of Hop1 is crucial for its function in meiosis, since mutation of conserved Cys371 to Ser in this motif results in a temperature-sensitive phenotype, which is defective in sporulation and meiosis. The direct role for Hop1 or its ZnF in the formation of joint molecules and checkpoint control over the progression of meiotic recombination intermediates is unknown. To understand the underlying biochemical mechanism, we constructed a series of recombination intermediates. Hop1 or its ZnF were able to bind different recombination intermediates. Interestingly, the binding affinity of Hop1 and its ZnF was much higher for the Holliday junction as compared to other recombination intermediates. The complexes of Hop1 or its ZnF with the Holliday junction were stable and specific as shown by NaCl titration and competition experiment. Hop1 and its ZnF blocked BLM helicase-induced unwinding of the Holliday junction, indicating that the interaction between Hop1 and its ZnF with the Holliday junction is specific. DNase I footprinting experiment showed that Hop1 or its ZnF bind to the center of the Holliday junction. 2-aminopurine fluorescence and KMnO4 experiments showed that Hop1 or its ZnF can distort the Holliday junction in a 2-fold symmetrical manner. The molecular modeling study showed that Hop1 ZnF folded into unique helix-loop-helix motif and bound to center of the Holliday junction. In summary, this study shows that Hop1 protein or its ZnF interact specifically with the Holliday junction and distort its structure. Taken together, these results implicate that Hop1 protein might coordinate the physical monitoring of meiotic recombination intermediates during the process of branch migration and that Hop1 ZnF acts as a structural determinant of Hop1 protein functions.

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Shahravan, Seyed Hesam. "In vitro and In vivo High-throughput Analysis of Protein:DNA Interactions." Thesis, 2012. http://hdl.handle.net/1807/33862.

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In this thesis, emphasis has been placed on development of new approaches for high-throughput analysis of protein:DNA interactions in vitro and in vivo. In vitro strategies for detection of protein:DNA interaction require isolation of active and soluble protein. However, current methodologies for purification of proteins often fail to provide high yield of pure and tag-free protein mainly because enzymatic cleavage reactions for tag removal do not exhibit stringent sequence specificity. Solving this problem is an important step towards high-throughput in vitro analysis of protein:DNA interactions. As a result, parts of this thesis are devoted to developing new approaches to enhance the specificity of a proteolysis reaction. The first approach was through manipulation of experimental conditions to maximize the yield of the desired protein products from enterokinase proteolysis reactions of two His-tagged proteins. Because it was suspected that accessibility of the EK site was impeded, that is, a structural problem due to multimerization of proteins, focus was based on use of denaturants as a way to open the structure, thereby essentially increasing the stoichiometry of the canonical recognition site over noncanonical, adventitious sites. Promoting accessibility of the canonical EK target site can increase proteolytic specificity and cleavage yield, and general strategies promoting a more open structure should be useful for preparation of proteins requiring endoprotease treatment. One such strategy for efficient EK proteolysis is proposed: by heterodimerizing with a separate leucine zipper, the bZIP basic region and amino-terminus can become more open and potentially more accessible to enterokinase. In vivo strategies have the advantage over their in vitro counterparts of providing a native-like environment for assessing protein:DNA interactions, yet the most frequently used techniques often suffer from high false-positive and false-negative rates. In this thesis, a new bioprobe system for high-throughput detection of protein:DNA interactions in vivo is presented. This system offers higher levels of accuracy and sensitivity as well as accessibility and ease of manipulation in comparison with existing technologies.

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Books on the topic "DNA binding protein; Yeast/CPF1"

1

McNeel, Douglas Gordon. Identification and characterization of TRF1: A DNA-binding protein in a yeast linear DNA plasmid system. 1992.

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Book chapters on the topic "DNA binding protein; Yeast/CPF1"

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Hofmann, J. F. X., and S. M. Gasser. "Protein-DNA Interaction at Yeast Replication Origins: an ARS Consensus Binding Protein." In DNA Replication: The Regulatory Mechanisms, 181–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-76988-7_17.

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Hofmann, J. F. X., M. Cockell, and S. M. Gasser. "Protein-DNA Interaction at Yeast Replication Origins: An ARS Consensus Binding Protein." In DNA Replication and the Cell Cycle, 79–91. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-77040-1_7.

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Klein, Peter, and Karl-Josef Dietz. "Identification of DNA-Binding Proteins and Protein-Protein Interactions by Yeast One-Hybrid and Yeast Two-Hybrid Screen." In Methods in Molecular Biology, 171–92. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-702-0_10.

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Wollman, Adam J. M., and Mark C. Leake. "Single-Molecule Narrow-Field Microscopy of Protein–DNA Binding Dynamics in Glucose Signal Transduction of Live Yeast Cells." In Methods in Molecular Biology, 5–15. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3631-1_2.

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Raychaudhuri, Soumya. "Protein Interaction Networks." In Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.003.0017.

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Genes and proteins interact with each other in many complicated ways. For example, proteins can interact directly with each other to form complexes or to modify each other so that their function is altered. Gene expression can be repressed or induced by transcription factor proteins. In addition there are countless other types of interactions. They constitute the key physiological steps in regulating or initiating biological responses. For example the binding of transcription factors to DNA triggers the assembly of the RNA assembly machinery that transcribes the mRNA that then is used as the template for protein production. Interactions such as these have been carefully elucidated and have been described in great detail in the scientific literature. Modern assays such as yeast-2-hybrid screens offer rapid means to ascertain many of the potential protein–protein interactions in an organism in a large-scale approach. In addition, other experimental modalities such as gene-expression array assays offer indirect clues about possible genetic interactions. One area that has been greatly explored in the bioinformatics literature is the possibility of learning genetic or protein networks, both from the scientific literature and from large-scale experimental data. Indeed, as we get to know more and more genes, it will become increasingly important to appreciate their interactions with each other. An understanding of the interactions between genes and proteins in a network allows for a meaningful global view of the organism and its physiology and is necessary to better understand biology. In this chapter we will explore methods to either (1) mine the scientific literature to identify documented genetic interactions and build networks of genes or (2) to confirm protein interactions that have been proposed experimentally. Our focus here is on direct physical protein–protein interactions, though the techniques described could be extended to any type of biological interaction between genes or proteins. There are multiple steps that must be addressed in identifying genetic interaction information contained within the text. After compiling the necessary documents and text, the first step is to identify gene and protein names in the text.

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