Disease gene characterization through large-scale co-expression analysis

PLoS ONE

Volumn 4, Issue 12, 2009, Pages

  Day, Allen ^a   Dong, Jun ^a   Funari, Vincent A ^a,b   Harry, Bret ^a   Strom, Samuel P ^a   Cohn, Dan H ^a,b   Nelson, Stanley F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b CEDARS SINAI MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BONE DYSPLASIA; CARTILAGE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC DATABASE; GENOMICS; INFORMATION RETRIEVAL; JOUBERT SYNDROME; LIMB GIRDLE MUSCULAR DYSTROPHY; MENTAL DISEASE; MICROCEPHALY; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; ANIMAL; BASE PAIRING; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENERAL ASPECTS OF DISEASE; GENETICS; HUMAN; MOUSE; REGRESSION ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ANIMALS; BASE PAIRING; CLUSTER ANALYSIS; DISEASE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REGRESSION ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 77949515984     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008491     Document Type: Article

References (70)

1. Ferrara C, Wang P, Neto E, Stevens R, Bain J, et al. (2008) Genetic networks of liver metabolism revealed by integration of metabolic and transcriptional profiling. PLoS Genet 4: e1000034.
2. Lee I, Lehner B, Crombie C, Wong W, Fraser A, et al. (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40: 181-188.
3. Steinhauser D, Usadel B, Luedemann A, Thimm O, Kopka J (2004) CSB.DB: a comprehensive systems-biology database. Bioinformatics 20: 3647-3651.
4. Steinhauser D, Junker B, Luedemann A, Selbig J, Kopka J (2004) Hypothesis- driven approach to predict transcriptional units from gene expression data. Bioinformatics 20: 1928-1939.
5. Schena M, Shalon D, Davis R, Brown P (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
6. Lockhart D, Dong H, Byrne M, Follettie M, Gallo M, et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14: 1675-1680.
7. Rock M, Prenen J, Funari V, Funari T, Merriman B, et al. (2008) Gain-of-function mutations in TRPV4 cause autosomal dominant brachyolmia. Nat Genet 40: 999-1003.
8. Tompson S, Merriman B, Funari V, Fresquet M, Lachman R, et al. (2009) A recessive skeletal dysplasia, SEMD aggrecan type, results from a missense mutation affecting the C-type lectin domain of aggrecan. Am J Hum Genet 84: 72-79.
9. Yu W, Wulf A, Liu T, Khoury M, Gwinn M (2008) Gene Prospector: an evidence gateway for evaluating potential susceptibility genes and interacting risk factors for human diseases. BMC Bioinformatics 9: 528.
10. Kohler S, Bauer S, Horn D, Robinson P (2008) Walking the interactome for prioritization of candidate disease genes. Am J Hum Genet 82: 949-958.
11. Adie E, Adams R, Evans K, Porteous D, Pickard B (2006) SUSPECTS: enabling fast and effective prioritization of positional candidates. Bioinformatics 22: 773-774.
12. Kobayashi N, Toyoda T (2008) Statistical search on the Semantic Web. Bioinformatics 24: 1002-1010.
13. Thornblad T, Elliott K, Jowett J, Visscher P (2007) Prioritization of positional candidate genes using multiple web-based software tools. Twin Res Hum Genet 10: 861-870.
14. Seelow D, Schwarz J, Schuelke M (2008) GeneDistiller-distilling candidate genes from linkage intervals. PLoS One 3: e3874.
15. Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, et al. (2006) Gene prioritization through genomic data fusion. Nat Biotechnol 24: 537-544.
16. Chen J, Bardes E, Aronow B, Jegga A (2009) ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res 37: W305-311.
17. Su A, Wiltshire T, Batalov S, Lapp H, Ching K, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
18. Nagarajan R, Le N, Mahoney H, Araki T, Milbrandt J (2002) Deciphering peripheral nerve myelination by using Schwann cell expression profiling. Proc Natl Acad Sci U S A 99: 8998-9003.
19. Rossi S, Masotti D, Nardini C, Bonora E, Romeo G, et al. (2006) TOM: a web- based integrated approach for identification of candidate disease genes. Nucleic Acids Res 34: W285-292.
20. Carlson M, Zhang B, Fang Z, Mischel P, Horvath S, et al. (2006) Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. BMC Genomics 7: 40.
21. Horvath S, Zhang B, Carlson M, Lu K, Zhu S, et al. (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci U S A 103: 17402-17407.
22. Shyamsundar R, Kim Y, Higgins J, Montgomery K, Jorden M, et al. (2005) A DNA microarray survey of gene expression in normal human tissues. Genome Biol 6: R22.
23. Greco D, Somervuo P, Di Lieto A, Raitila T, Nitsch L, et al. (2008) Physiology, pathology and relatedness of human tissues from gene expression meta-analysis. PLoS One 3: e1880.
24. Wang Y, Miller D, Clarke R (2008) Approaches to working in high-dimensional data spaces: gene expression microarrays. Br J Cancer 98: 1023-1028.
25. Rhodes D, Yu J, Shanker K, Deshpande N, Varambally R, et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 6: 1-6.
26. Wilson B, Giguère V (2007) Identification of novel pathway partners of p68 and p72 RNA helicases through Oncomine meta-analysis. BMC Genomics 8: 419.
27. Rhodes D, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, et al. (2007) Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia 9: 166-180.
28. Liang S, Li Y, Be X, Howes S, Liu W (2006) Detecting and profiling tissue- selective genes. Physiol Genomics 26: 158-162.
29. Whetzel P, Parkinson H, Causton H, Fan L, Fostel J, et al. (2006) The MGED Ontology: a resource for semantics-based description of microarray experiments. Bioinformatics 22: 866-873.
30. Spellman P, Miller M, Stewart J, Troup C, Sarkans U, et al. (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 3: RESEARCH0046.
31. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, et al. (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29: 365-371.
32. Day A, Carlson M, Dong J, O'Connor B, Nelson S (2007) Celsius: a community resource for Affymetrix microarray data. Genome Biol 8: R112.
33. Funari V, Day A, Krakow D, Cohn Z, Chen Z, et al. (2007) Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression. BMC Genomics 8: 165.
34. Liu G, Loraine A, Shigeta R, Cline M, Cheng J, et al. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res 31: 82-86.
35. Zhu J, Sanborn J, Benz S, Szeto C, Hsu F, et al. (2009) The UCSC Cancer Genomics Browser. Nat Methods 6: 239-240.
36. Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
37. Harris M, Clark J, Ireland A, Lomax J, Ashburner M, et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: D258-261.
38. Irizarry R, Bolstad B, Collin F, Cope L, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.
39. McKusick V (2007) Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80: 588-604.
40. Bult C, Eppig J, Kadin J, Richardson J, Blake J (2008) The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res 36: D724-728.
41. Muragaki Y, Mariman E, van Beersum S, Perälä M, van Mourik J, et al. (1996) A mutation in the gene encoding the alpha 2 chain of the fibril-associated collagen IX, COL9A2, causes multiple epiphyseal dysplasia (EDM2). Nat Genet 12: 103-105.
42. Valente E, Brancati F, Dallapiccola B (2008) Genotypes and phenotypes of Joubert syndrome and related disorders. Eur J Med Genet 51: 1-23.
43. Jackson A, McHale D, Campbell D, Jafri H, Rashid Y, et al. (1998) Primary autosomal recessive microcephaly (MCPH1) maps to chromosome 8p22-pter. Am J Hum Genet 63: 541-546.
44. Guglieri M, Straub V, Bushby K, Lochmuller H (2008) Limb-girdle muscular dystrophies. Curr Opin Neurol 21: 576-584.
45. Utsch B, Sayer J, Attanasio M, Pereira R, Eccles M, et al. (2006) Identification of the first AHI1 gene mutations in nephronophthisis-associated Joubert syndrome. Pediatr Nephrol 21: 32-35.
46. Parisi M, Bennett C, Eckert M, Dobyns W, Gleeson J, et al. (2004) The NPHP1 gene deletion associated with juvenile nephronophthisis is present in a subset of individuals with Joubert syndrome. Am J Hum Genet 75: 82-91.
47. Valente E, Silhavy J, Brancati F, Barrano G, Krishnaswami S, et al. (2006) Mutations in CEP290, which encodes a centrosomal protein, cause pleiotropic forms of Joubert syndrome. Nat Genet 38: 623-625.
48. Delous M, Baala L, Salomon R, Laclef C, Vierkotten J, et al. (2007) The ciliary gene RPGRIP1L is mutated in cerebello-oculo-renal syndrome (Joubert syndrome type B) and Meckel syndrome. Nat Genet 39: 875-881.
49. Baala L, Romano S, Khaddour R, Saunier S, Smith U, et al. (2007) The Meckel-Gruber syndrome gene, MKS3, is mutated in Joubert syndrome. Am J Hum Genet 80: 186-194.
50. Bielas S, Silhavy J, Brancati F, Kisseleva M, Al-Gazali L, et al. (2009) Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies. Nat Genet 41: 1032-1036.
51. Dixon-Salazar T, Silhavy J, Marsh S, Louie C, Scott L, et al. (2004) Mutations in the AHI1 gene, encoding jouberin, cause Joubert syndrome with cortical polymicrogyria. Am J Hum Genet 75: 979-987.
52. Ferland R, Eyaid W, Collura R, Tully L, Hill R, et al. (2004) Abnormal cerebellar development and axonal decussation due to mutations in AHI1 in Joubert syndrome. Nat Genet 36: 1008-1013.
53. Sayer J, Otto E, O'Toole J, Nurnberg G, Kennedy M, et al. (2006) The centrosomal protein nephrocystin-6 is mutated in Joubert syndrome and activates transcription factor ATF4. Nat Genet 38: 674-681.
54. Arts H, Doherty D, van Beersum S, Parisi M, Letteboer S, et al. (2007) Mutations in the gene encoding the basal body protein RPGRIP1L, a nephrocystin-4 interactor, cause Joubert syndrome. Nat Genet 39: 882-888.
55. Keeler L, Marsh S, Leeflang E, Woods C, Sztriha L, et al. (2003) Linkage analysis in families with Joubert syndrome plus oculo-renal involvement identifies the CORS2 locus on chromosome 11p12-q13.3. Am J Hum Genet 73: 656-662.
56. Valente E, Salpietro D, Brancati F, Bertini E, Galluccio T, et al. (2003) Description, nomenclature, and mapping of a novel cerebello-renal syndrome with the molar tooth malformation. Am J Hum Genet 73: 663-670.
57. Valente E, Marsh S, Castori M, Dixon-Salazar T, Bertini E, et al. (2005) Distinguishing the four genetic causes of Jouberts syndrome-related disorders. Ann Neurol 57: 513-519.
58. Bailey A, Le Couteur A, Gottesman I, Bolton P, Simonoff E, et al. (1995) Autism as a strongly genetic disorder: evidence from a British twin study. Psychol Med 25: 63-77.
59. Ritvo E, Ritvo R, Freeman B (1991) Debate and argument. Concordance for the syndrome of autism. J Child Psychol Psychiatry 32: 1031-1034.
60. Abrahams B, Geschwind D (2008) Advances in autism genetics: on the threshold of a new neurobiology. Nat Rev Genet 9: 341-355.
61. Goh K, Cusick M, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
62. Kumar R, KaraMohamed S, Sudi J, Conrad D, Brune C, et al. (2008) Recurrent 16p11.2 microdeletions in autism. Hum Mol Genet 17: 628-638.
63. Strom S, Stone J, Ten Bosch J, Merriman B, Cantor R, et al. (2009) High- density SNP association study of the 17q21 chromosomal region linked to autism identifies CACNA1G as a novel candidate gene. Mol Psychiatry.
64. Maestrini E, Pagnamenta A, Lamb J, Bacchelli E, Sykes N, et al. (2009) High- density SNP association study and copy number variation analysis of the AUTS1 and AUTS5 loci implicate the IMMP2L-DOCK4 gene region in autism susceptibility. Mol Psychiatry.
65. Stopkova P, Vevera J, Paclt I, Zukov I, Lachman H (2004) Analysis of SYNJ1, a candidate gene for 21q22 linked bipolar disorder: a replication study. Psychiatry Res 127: 157-161.
66. Hans M, Luvisetto S, Williams M, Spagnolo M, Urrutia A, et al. (1999) Functional consequences of mutations in the human alpha1A calcium channel subunit linked to familial hemiplegic migraine. J Neurosci 19: 1610-1619.
67. Verma R, Holmans P, Knowles J, Grover D, Evgrafov O, et al. (2008) Linkage disequilibrium mapping of a chromosome 15q25-26 major depression linkage region and sequencing of NTRK3. Biol Psychiatry 63: 1185-1189.
68. de Carvalho Aguiar P, Sweadner K, Penniston J, Zaremba J, Liu L, et al. (2004) Mutations in the Na+/K+ -ATPase alpha3 gene ATP1A3 are associated with rapid-onset dystonia parkinsonism. Neuron 43: 169-175.
69. Carroll L, Williams N, Moskvina V, Russell E, Norton N, et al. (2009) Evidence for rare and common genetic risk variants for schizophrenia at protein kinase C, alpha. Mol Psychiatry.
70. Brzustowicz L (2008) NOS1AP in schizophrenia. Curr Psychiatry Rep 10: 158-163.