References

Bagga, Paramjeet. S. Bioinformatics, Genomics, Proteomics. November 15, 2019. Ramapo College of New Jersey.
“XPA_1 Viewer.” EPD, epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=XPA_1.
“AceView: Gene:XPA, a Comprehensive Annotation of Human, Mouse and Worm Genes with MRNAs or ESTsAceView.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=xpa&submit=Go.
“iCn3D: Web-Based 3D Structure Viewer.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?showanno=1&mmdbid=57700.
Ikegami, et al. “Solution Structure of the DNA- and RPA-Binding Domain of the Human Repair Factor XPA.” Nat.Struct.Mol.Biol., www.rcsb.org/structure/1XPA.
Team, EBI Web. “PDBsum Entry 1xpa.” Secondary Structure: 1xpa, www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1xpa&template=protein.html&r=wiring&l=1&chain=A.
“PDBj 1XPA.” Protein Database of Japan, 13 July 2011, pdbj.org/mine/summary/1xpa.
“CDD Conserved Protein Domain Family: XPA_C.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/cdd/cl27062.
“CDD Conserved Protein Domain Family: XPA_N.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=307450.
“Family: XPA_C (PF05181).” Pfam: Protein Families , pfam.xfam.org/family/PF05181#tabview=tab0.
UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics. “DNA Repair Protein Complementing XP-A Cells.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, 13 Nov. 2019, www.uniprot.org/uniprot/P23025.
Krasikova, Yuliya S., et al. “RPA and XPA Interaction with DNA Structures Mimicking Intermediates of the Late Stages in Nucleotide Excision Repair.” PLOS ONE, Public Library of Science, journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0190782.
“Platinum Drug Resistance.” KEGG: Kyoto Encyclopedia of Genes and Genomes, GenomeNet, www.genome.jp/kegg-bin/show_pathway?hsa01524%2B7507.
“Nucleotide Excision Repair.” KEGG: Kyoto Encyclopedia of Genes and Genomes, GenomeNet, www.genome.jp/kegg-bin/show_pathway?hsa03420%2B7507.
Sugitani, Norie, et al. “XPA: A Key Scaffold for Human Nucleotide Excision Repair.” DNA Repair, U.S. National Library of Medicine, Aug. 2016, www.ncbi.nlm.nih.gov/pmc/articles/PMC4958585/.
“Xeroderma Pigmentosum Group A Complementing Protein.” Xeroderma Pigmentosum Group A Complementing Protein, Human Protein Reference Database, hprd.org/summary?hprd_id=02045&isoform_id=02045_1&isoform_name=.
“Gene: XPA: Homo Sapiens (Human).” Gene: XPA - ENSG00000136936, Bgee, bgee.org/?page=gene&gene_id=ENSG00000136936.
“XPA Gene (Protein Coding): DNA Damage Recognition And Repair Factor.” GeneCards, The Human Gene Database, www.genecards.org/cgi-bin/carddisp.pl?gene=XPA&keywords=XPA.
“RNA Helicase Aquarius.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/O60306.
“DNA Polymerase Epsilon Subunit 2.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/P56282.
“Replication Protein A 14 KDa Subunit.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/P35244.
“E3 Ubiquitin-Protein Ligase RBX1.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 13 Nov. 2019, www.uniprot.org/uniprot/P62877.
“E3 SUMO-Protein Ligase PIAS1.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 13 Nov. 2019, www.uniprot.org/uniprot/O75925.
“XPA XPA, DNA Damage Recognition and Repair Factor [Homo Sapiens (Human)] - Gene - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/gene/7507.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), RefS - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NG_011642.1?from=5001&to=27501&report=genbank.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NM_000380.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NM_001354975.1.
“DNA Repair Protein Complementing XP-A Cells Isoform 1 [Homo Sapiens] - Protein - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/protein/NP_000371.1.
Spivak, Graciela. “Nucleotide Excision Repair in Humans.” DNA Repair, U.S. National Library of Medicine, Dec. 2015, www.ncbi.nlm.nih.gov/pmc/articles/PMC4688078/?report=reader.
“XERODERMA PIGMENTOSUM, COMPLEMENTATION GROUP A; XPA.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/278700.
“Small Cell Cancer of the Lung.” OMIM, Online Mendelian Inheritance in Mans, omim.org/entry/182280?search=Small%2BCell%2BCarcinoma&highlight=%28carcinoma%7Ccarcinomatous%29%2Bcell%2Bsmall.
“Colorectal Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/114500?search=colorectal%2Bneoplasm&highlight=%28colorectal%7Ccolourectal%29%2Bneoplasm.
Lawania, Shweta, et al. “Association of XPA Polymorphisms Towards Lung Cancer Susceptibility and Its Predictive Role in Overall Survival of North Indians.” Biochemical Genetics, U.S. National Library of Medicine, Aug. 2018, www.ncbi.nlm.nih.gov/pubmed/29516319.
“Breast Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/114480?search=breast%2Bcancer&highlight=%28cancer%7Ccancerous%29%2Bbreast.
Dammann, Reinhard, et al. “Epigenetic Inactivation of a RAS Association Domain Family Protein from the Lung Tumour Suppressor Locus 3p21.3.” Nature News, Nature Publishing Group, www.nature.com/articles/ng0700_315.
Lawania, Shweta, et al. “Association of XPA Polymorphisms Towards Lung Cancer Susceptibility and Its Predictive Role in Overall Survival of North Indians.” Biochemical Genetics, U.S. National Library of Medicine, Aug. 2018, www.ncbi.nlm.nih.gov/pubmed/29516319.
“Lung Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/211980?search=Lung%2BCarcinoma&highlight=%28carcinoma%7Ccarcinomatous%29%2B%28lung%7Cpulmonary%7Cpulmonic%29.
“Gene: XPA.” Summary - Homo Sapiens - Ensembl Genome Browser 98, Ensembl, useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core%3Bg.
“Structure Analysis of 1XPA.” PDB Europe, Protein Databank in Europe, www.ebi.ac.uk/pdbe/entry/pdb/1xpa/analysis.
“Expression Atlas XPA.” Gene Expression Across Species and Biological Conditions, Ensembl, www.ebi.ac.uk/gxa/genes/ENSG00000136936?bs=%7B%22homo%2Bsapiens%22%3A%5B%22DEVELOPMENTAL_STAGE%22%2C%22AGE%22%5D%7D&ds=%7B%22kingdom%22%3A%5B%22animals%22%5D%7D#baseline.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149091.1.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149092.1.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149093.1.
“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149094.1.

Analysis of DNA damage recognition and repair factor (XPA) in Homo sapiens

Jeffrey Chimenti & Rory Vanderberg

Published: December 9, 2019

References

Bagga, Paramjeet. S. Bioinformatics, Genomics, Proteomics. November 15, 2019. Ramapo College of New Jersey.

“XPA_1 Viewer.” EPD, epd.epfl.ch/cgi-bin/get_doc?db=hgEpdNew&format=genome&entry=XPA_1.

“AceView: Gene:XPA, a Comprehensive Annotation of Human, Mouse and Worm Genes with MRNAs or ESTsAceView.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=xpa&submit=Go.

“iCn3D: Web-Based 3D Structure Viewer.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?showanno=1&mmdbid=57700.

Ikegami, et al. “Solution Structure of the DNA- and RPA-Binding Domain of the Human Repair Factor XPA.” Nat.Struct.Mol.Biol., www.rcsb.org/structure/1XPA.

Team, EBI Web. “PDBsum Entry 1xpa.” Secondary Structure: 1xpa, www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1xpa&template=protein.html&r=wiring&l=1&chain=A.

“PDBj 1XPA.” Protein Database of Japan, 13 July 2011, pdbj.org/mine/summary/1xpa.

“CDD Conserved Protein Domain Family: XPA_C.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/cdd/cl27062.

“CDD Conserved Protein Domain Family: XPA_N.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=307450.

“Family: XPA_C (PF05181).” Pfam: Protein Families , pfam.xfam.org/family/PF05181#tabview=tab0.

Krasikova, Yuliya S., et al. “RPA and XPA Interaction with DNA Structures Mimicking Intermediates of the Late Stages in Nucleotide Excision Repair.” PLOS ONE, Public Library of Science, journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0190782.

“Platinum Drug Resistance.” KEGG: Kyoto Encyclopedia of Genes and Genomes, GenomeNet, www.genome.jp/kegg-bin/show_pathway?hsa01524%2B7507.

“Nucleotide Excision Repair.” KEGG: Kyoto Encyclopedia of Genes and Genomes, GenomeNet, www.genome.jp/kegg-bin/show_pathway?hsa03420%2B7507.

Sugitani, Norie, et al. “XPA: A Key Scaffold for Human Nucleotide Excision Repair.” DNA Repair, U.S. National Library of Medicine, Aug. 2016, www.ncbi.nlm.nih.gov/pmc/articles/PMC4958585/.

“Xeroderma Pigmentosum Group A Complementing Protein.” Xeroderma Pigmentosum Group A Complementing Protein, Human Protein Reference Database, hprd.org/summary?hprd_id=02045&isoform_id=02045_1&isoform_name=.

“Gene: XPA: Homo Sapiens (Human).” Gene: XPA - ENSG00000136936, Bgee, bgee.org/?page=gene&gene_id=ENSG00000136936.

“XPA Gene (Protein Coding): DNA Damage Recognition And Repair Factor.” GeneCards, The Human Gene Database, www.genecards.org/cgi-bin/carddisp.pl?gene=XPA&keywords=XPA.

“RNA Helicase Aquarius.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/O60306.

“DNA Polymerase Epsilon Subunit 2.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/P56282.

“Replication Protein A 14 KDa Subunit.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 16 Oct. 2019, www.uniprot.org/uniprot/P35244.

“E3 Ubiquitin-Protein Ligase RBX1.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 13 Nov. 2019, www.uniprot.org/uniprot/P62877.

“E3 SUMO-Protein Ligase PIAS1.” UniProt ConsortiumEuropean Bioinformatics InstituteProtein Information ResourceSIB Swiss Institute of Bioinformatics, UniProtKB, 13 Nov. 2019, www.uniprot.org/uniprot/O75925.

“XPA XPA, DNA Damage Recognition and Repair Factor [Homo Sapiens (Human)] - Gene - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/gene/7507.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), RefS - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NG_011642.1?from=5001&to=27501&report=genbank.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NM_000380.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NM_001354975.1.

“DNA Repair Protein Complementing XP-A Cells Isoform 1 [Homo Sapiens] - Protein - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/protein/NP_000371.1.

Spivak, Graciela. “Nucleotide Excision Repair in Humans.” DNA Repair, U.S. National Library of Medicine, Dec. 2015, www.ncbi.nlm.nih.gov/pmc/articles/PMC4688078/?report=reader.

“XERODERMA PIGMENTOSUM, COMPLEMENTATION GROUP A; XPA.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/278700.

“Small Cell Cancer of the Lung.” OMIM, Online Mendelian Inheritance in Mans, omim.org/entry/182280?search=Small%2BCell%2BCarcinoma&highlight=%28carcinoma%7Ccarcinomatous%29%2Bcell%2Bsmall.

“Colorectal Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/114500?search=colorectal%2Bneoplasm&highlight=%28colorectal%7Ccolourectal%29%2Bneoplasm.

Lawania, Shweta, et al. “Association of XPA Polymorphisms Towards Lung Cancer Susceptibility and Its Predictive Role in Overall Survival of North Indians.” Biochemical Genetics, U.S. National Library of Medicine, Aug. 2018, www.ncbi.nlm.nih.gov/pubmed/29516319.

“Breast Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/114480?search=breast%2Bcancer&highlight=%28cancer%7Ccancerous%29%2Bbreast.

Dammann, Reinhard, et al. “Epigenetic Inactivation of a RAS Association Domain Family Protein from the Lung Tumour Suppressor Locus 3p21.3.” Nature News, Nature Publishing Group, www.nature.com/articles/ng0700_315.

Lawania, Shweta, et al. “Association of XPA Polymorphisms Towards Lung Cancer Susceptibility and Its Predictive Role in Overall Survival of North Indians.” Biochemical Genetics, U.S. National Library of Medicine, Aug. 2018, www.ncbi.nlm.nih.gov/pubmed/29516319.

“Lung Cancer.” OMIM, Online Mendelian Inheritance in Man, omim.org/entry/211980?search=Lung%2BCarcinoma&highlight=%28carcinoma%7Ccarcinomatous%29%2B%28lung%7Cpulmonary%7Cpulmonic%29.

“Gene: XPA.” Summary - Homo Sapiens - Ensembl Genome Browser 98, Ensembl, useast.ensembl.org/Homo_sapiens/Gene/Summary?db=core%3Bg.

“Structure Analysis of 1XPA.” PDB Europe, Protein Databank in Europe, www.ebi.ac.uk/pdbe/entry/pdb/1xpa/analysis.

“Expression Atlas XPA.” Gene Expression Across Species and Biological Conditions, Ensembl, www.ebi.ac.uk/gxa/genes/ENSG00000136936?bs=%7B%22homo%2Bsapiens%22%3A%5B%22DEVELOPMENTAL_STAGE%22%2C%22AGE%22%5D%7D&ds=%7B%22kingdom%22%3A%5B%22animals%22%5D%7D#baseline.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149091.1.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149092.1.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149093.1.

“Homo Sapiens XPA, DNA Damage Recognition and Repair Factor (XPA), Tran - Nucleotide - NCBI.” National Center for Biotechnology Information, U.S. National Library of Medicine, www.ncbi.nlm.nih.gov/nuccore/NR_149094.1.