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diff --git a/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 b/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 index 09d1513..accd8c0 100644 --- a/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 +++ b/gnqa/paper2_eval/data/dataset/domain_expert_aging_4 @@ -62,4 +62,132 @@ ], "answer": "Genes typically associated with early aging include those involved in segmental progeroid syndromes, such as the Werner syndrome gene [2]. Additionally, genes critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway, are also associated with early aging [2].", "question": "which genes are typically associated with early aging?" +}{ + "titles": [ + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2009 - The Human Ageing Genomic Resources online.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2011 - Clinical aspects and molecular diagnostics of skin aging.pdf", + "2015 - Transcriptomic profiles of aging in purified.pdf", + "2004 - A Transcriptional Profile of Aging.pdf", + "2020 - A multidimensional systems biology.pdf", + "2011 - Metabolism, Genomics, and DNA Repair in the Mouse Aging Liver.pdf", + "2010 - MicroRNA, mRNA, and protein expression link.pdf", + "2012 - GeneFriends An online co-expression analysis.pdf" + ], + "extraction_id": [ + "d59d7882-333d-5576-86ab-3cfa6354b946", + "52c67b46-63f2-54ae-a78e-e9d54a55f6e4", + "d59d7882-333d-5576-86ab-3cfa6354b946", + "674e1da7-73d5-5101-b5a5-4981e483123c", + "e5fd1ff0-8df5-577f-9f2d-31b0941d5ce5", + "8b47c304-ee91-5c52-8324-79fd0bd32b27", + "9d1656aa-32d2-5094-8232-4817655b1cbd", + "a6a6b5ba-3a72-55c5-91bb-abe747624348", + "fc9974c9-2e48-5a08-9112-0109df9ce096", + "1839dfa6-7080-5de4-96cb-3493ca2056d3" + ], + "document_id": [ + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e32f8f2c-d3ad-5dae-a393-9bd87c370ebe", + "50f357a3-e0f2-5e32-a6b2-771fb4b1e1c6", + "4ab656a7-9656-526b-94e1-422875409b44", + "d040bfe3-e409-5b5c-b8f8-f3dd4fc060e3", + "a94fd15d-373e-51c5-ad74-a17e4260d32a", + "c3ae47b0-42dd-5ab0-8fec-a41831d1bbfa", + "be20af52-c782-5098-893a-9a92000bf5a0" + ], + "id": [ + "chatcmpl-ABLwhCwS1z9hZBn1zWSbHm5JcD7CF", + "b719fbc0-94e4-5df0-abb7-0d13fc36214c", + "8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb", + "413f8f54-b5cc-5089-9f5c-d9e3b8bcf594", + "896169ed-4b9b-5ebc-9c9d-1cd2e6f3437c", + "6b4fb407-fd3f-52a3-9cfd-07dc5c891dd5", + "17ce11f7-55df-59bd-a801-a6f38ae9a9ef", + "61baeaa5-d65a-54b5-bfee-9bab8bbf1985", + "3414ff44-7d60-5492-9956-353ab9a94a43", + "b2d47567-09dc-5c77-be72-9448aa954e6b", + "1c3f7772-e1fa-5063-bda7-04b2f7e7b0e3" + ], + "contexts": [ + "lar signatures of mammalian aging. Some of the genes", + "www.ncbi.nlm.nih.gov/homologene) of genes strongly asso-ciated with aging in model organisms. Also included are genesin which mutations result in segmental progeroid syndromes,such as the Werners syndrome gene, as well as genes criticalin pathways previously related to aging, such as the insulin/insulin-like signalling pathway (de Magalhes et al ., 2005a). The", + "overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,", + "expression profile of aging in human muscle. Physiol Genomics 2003;14:149-59. 142. Rodwell GE, Sonu R, Zahn JM. A transcriptional profile of aging inthe human kidney. PLoS Biol 2004;e427:2. 143. Hasty P, Campisi J, Hoeijmakers J, van Steeg H, Vijg J. Aging and genome maintenance: lessons from the mouse? Science 2003;299:1355-9. 144. Kyng KJ, May A, Klvraa S, Bohr VA. Gene expression profiling in Werner syndrome closely resembles that of normal aging. Proc Natl Acad Sci U S A 2003;100:12259-64.", + "neurodegenerative diseases. Nature. 2006;443:787 95. 50. de Magalhes JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009;25:875 81. 51. Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, et al. AGEMAP: a gene expression database for aging in mice. PLoS Genet. 2007;3:e201. 52. Liu LF, Shen WJ, Ueno M, Patel S, Kraemer FB. Characterization of age- related gene expression profiling in bone marrow and epididymal", + "Ly DH, Lockhart DJ, Lerner RA, Schultz PG (2000) Mitotic misregulation and human aging. Science 287: 24862492. McCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, et al. (2004) Comparing genomic expression patterns across species identies shared transcriptional prole in aging. Nat Genet 36: 197204. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, et al. (2003) Genes that act downstream of DAF-16 to inuence the lifespan of Caenorhabditis elegans Nature 424: 277283.", + "genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build", + "exhibits important alterations in global gene expressionproles with age. In mice, aging is accompanied by changesin expression of genes associated with increased inamma-tion, cellular stress, brosis, altered capacity for apoptosis,xenobiotic metabolism, normal cell-cycle control, and DNAreplication [ 5]. Lifelong calorie restriction reversed the", + "stance, genes associated with energy production, which decrease their expression during aging across various tissues and species (Zahn et al. 2006, 2007; de Magalha es et al. 2009), start decreasing at this transition point in our data (group 5; Fig. 2A). Hence, 25 yr of age in humans may mark the beginning of systemic change associated with certain senescence processes. Conservation of expression changes with age We observe that both developmental and aging expression pro-", + "p <10 -6; Table 1 shows the top 25 genes. Many of these genes have been associated with age-related diseases.Several other genes that have been shown to play a role in aging such as lysosomal-associated membrane protein-2 Lamp2 [19] (p = 5.68 -30), Fas [20] (p = 2.70-31) and growth hormone receptor Ghr [21] (p = 1.34-19) also showed a significant co-expression. Anxa2, Anxa3 and Anxa4 also show a low p-value (p < 10-25) as well as several S100 calcium binding proteins which have been" + ], + "answer": "Genes typically associated with early aging include those involved in segmental progeroid syndromes, such as the Werner syndrome gene [2]. Additionally, genes critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway, are also associated with early aging [2].", + "question": "which genes are typically associated with early aging?" +}{ + "titles": [ + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2009 - The Human Ageing Genomic Resources online.pdf", + "2012 - Genome-Environment Interactions That Modulate.pdf", + "2011 - Clinical aspects and molecular diagnostics of skin aging.pdf", + "2015 - Transcriptomic profiles of aging in purified.pdf", + "2004 - A Transcriptional Profile of Aging.pdf", + "2020 - A multidimensional systems biology.pdf", + "2011 - Metabolism, Genomics, and DNA Repair in the Mouse Aging Liver.pdf", + "2010 - MicroRNA, mRNA, and protein expression link.pdf", + "2012 - GeneFriends An online co-expression analysis.pdf" + ], + "extraction_id": [ + "d59d7882-333d-5576-86ab-3cfa6354b946", + "52c67b46-63f2-54ae-a78e-e9d54a55f6e4", + "d59d7882-333d-5576-86ab-3cfa6354b946", + "674e1da7-73d5-5101-b5a5-4981e483123c", + "e5fd1ff0-8df5-577f-9f2d-31b0941d5ce5", + "8b47c304-ee91-5c52-8324-79fd0bd32b27", + "9d1656aa-32d2-5094-8232-4817655b1cbd", + "a6a6b5ba-3a72-55c5-91bb-abe747624348", + "fc9974c9-2e48-5a08-9112-0109df9ce096", + "1839dfa6-7080-5de4-96cb-3493ca2056d3" + ], + "document_id": [ + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e43cd3b6-ad8e-5422-ba7c-ceb6e66cc529", + "b1a1997c-e9df-5dc0-9d12-a3977d0c64ec", + "e32f8f2c-d3ad-5dae-a393-9bd87c370ebe", + "50f357a3-e0f2-5e32-a6b2-771fb4b1e1c6", + "4ab656a7-9656-526b-94e1-422875409b44", + "d040bfe3-e409-5b5c-b8f8-f3dd4fc060e3", + "a94fd15d-373e-51c5-ad74-a17e4260d32a", + "c3ae47b0-42dd-5ab0-8fec-a41831d1bbfa", + "be20af52-c782-5098-893a-9a92000bf5a0" + ], + "id": [ + "chatcmpl-ABLwhCwS1z9hZBn1zWSbHm5JcD7CF", + "b719fbc0-94e4-5df0-abb7-0d13fc36214c", + "8fd5ab85-67ed-55e6-bbfa-09436c4fdbfb", + "413f8f54-b5cc-5089-9f5c-d9e3b8bcf594", + "896169ed-4b9b-5ebc-9c9d-1cd2e6f3437c", + "6b4fb407-fd3f-52a3-9cfd-07dc5c891dd5", + "17ce11f7-55df-59bd-a801-a6f38ae9a9ef", + "61baeaa5-d65a-54b5-bfee-9bab8bbf1985", + "3414ff44-7d60-5492-9956-353ab9a94a43", + "b2d47567-09dc-5c77-be72-9448aa954e6b", + "1c3f7772-e1fa-5063-bda7-04b2f7e7b0e3" + ], + "contexts": [ + "lar signatures of mammalian aging. Some of the genes", + "www.ncbi.nlm.nih.gov/homologene) of genes strongly asso-ciated with aging in model organisms. Also included are genesin which mutations result in segmental progeroid syndromes,such as the Werners syndrome gene, as well as genes criticalin pathways previously related to aging, such as the insulin/insulin-like signalling pathway (de Magalhes et al ., 2005a). The", + "overexpressed with age seem to be a response to aging,in that they have been previously found to have protec-tive functions (de Magalha es et al., 2009b). As such,these genes may help organisms manage aging andcould be targets for manipulation. Likewise, gene ex-pression analysis of CR has been conducted to identifyassociated genes (Lee et al., 1999, 2000). A number ofmolecular signatures have emerged from such studiesthat could be useful to identify candidate processes andpathways that affect aging,", + "expression profile of aging in human muscle. Physiol Genomics 2003;14:149-59. 142. Rodwell GE, Sonu R, Zahn JM. A transcriptional profile of aging inthe human kidney. PLoS Biol 2004;e427:2. 143. Hasty P, Campisi J, Hoeijmakers J, van Steeg H, Vijg J. Aging and genome maintenance: lessons from the mouse? Science 2003;299:1355-9. 144. Kyng KJ, May A, Klvraa S, Bohr VA. Gene expression profiling in Werner syndrome closely resembles that of normal aging. Proc Natl Acad Sci U S A 2003;100:12259-64.", + "neurodegenerative diseases. Nature. 2006;443:787 95. 50. de Magalhes JP, Curado J, Church GM. Meta-analysis of age-related gene expression profiles identifies common signatures of aging. Bioinformatics. 2009;25:875 81. 51. Zahn JM, Poosala S, Owen AB, Ingram DK, Lustig A, Carter A, et al. AGEMAP: a gene expression database for aging in mice. PLoS Genet. 2007;3:e201. 52. Liu LF, Shen WJ, Ueno M, Patel S, Kraemer FB. Characterization of age- related gene expression profiling in bone marrow and epididymal", + "Ly DH, Lockhart DJ, Lerner RA, Schultz PG (2000) Mitotic misregulation and human aging. Science 287: 24862492. McCarroll SA, Murphy CT, Zou S, Pletcher SD, Chin CS, et al. (2004) Comparing genomic expression patterns across species identies shared transcriptional prole in aging. Nat Genet 36: 197204. Murphy CT, McCarroll SA, Bargmann CI, Fraser A, Kamath RS, et al. (2003) Genes that act downstream of DAF-16 to inuence the lifespan of Caenorhabditis elegans Nature 424: 277283.", + "genes driving cellular senescence, and perform various integrative analyses. Genes inducing cellular senescence tend to be overexpressed with age in human tissues and are significantly overrepresented in anti-longevity and tumor-suppressor genes, while genes inhibiting cellular senescence overlap with pro-longevity and oncogenes. Furthermore, cellular senescence genes are strongly conserved in mammals but not in invertebrates. We also build", + "exhibits important alterations in global gene expressionproles with age. In mice, aging is accompanied by changesin expression of genes associated with increased inamma-tion, cellular stress, brosis, altered capacity for apoptosis,xenobiotic metabolism, normal cell-cycle control, and DNAreplication [ 5]. Lifelong calorie restriction reversed the", + "stance, genes associated with energy production, which decrease their expression during aging across various tissues and species (Zahn et al. 2006, 2007; de Magalha es et al. 2009), start decreasing at this transition point in our data (group 5; Fig. 2A). Hence, 25 yr of age in humans may mark the beginning of systemic change associated with certain senescence processes. Conservation of expression changes with age We observe that both developmental and aging expression pro-", + "p <10 -6; Table 1 shows the top 25 genes. Many of these genes have been associated with age-related diseases.Several other genes that have been shown to play a role in aging such as lysosomal-associated membrane protein-2 Lamp2 [19] (p = 5.68 -30), Fas [20] (p = 2.70-31) and growth hormone receptor Ghr [21] (p = 1.34-19) also showed a significant co-expression. Anxa2, Anxa3 and Anxa4 also show a low p-value (p < 10-25) as well as several S100 calcium binding proteins which have been" + ], + "answer": "Genes typically associated with early aging include those involved in segmental progeroid syndromes, such as the Werner syndrome gene [2]. Additionally, genes critical in pathways previously related to aging, such as the insulin/insulin-like signaling pathway, are also associated with early aging [2].", + "question": "which genes are typically associated with early aging?" }
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