Caron H, van Schaik B, van der MM, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voute PA, Heisterkamp S, van Kampen A, Versteeg R: The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science. 2001, 291: 1289-1292. 10.1126/science.1056794.
Article
CAS
PubMed
Google Scholar
Lercher MJ, Urrutia AO, Pavlicek A, Hurst LD: A unification of mosaic structures in the human genome. Hum Mol Genet. 2003, 12: 2411-2415. 10.1093/hmg/ddg251.
Article
CAS
PubMed
Google Scholar
Versteeg R, van Schaik BD, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AH: The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. Genome Res. 2003, 13: 1998-2004. 10.1101/gr.1649303.
Article
CAS
PubMed Central
PubMed
Google Scholar
Lercher MJ, Urrutia AO, Hurst LD: Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet. 2002, 31: 180-183. 10.1038/ng887.
Article
CAS
PubMed
Google Scholar
Bortoluzzi S, Rampoldi L, Simionati B, Zimbello R, Barbon A, d'Alessi F, Tiso N, Pallavicini A, Toppo S, Cannata N, Valle G, Lanfranchi G, Danieli GA: A comprehensive, high-resolution genomic transcript map of human skeletal muscle. Genome Res. 1998, 8: 817-825.
CAS
PubMed Central
PubMed
Google Scholar
Yamashita T, Honda M, Takatori H, Nishino R, Hoshino N, Kaneko S: Genome-wide transcriptome mapping analysis identifies organ-specific gene expression patterns along human chromosomes. Genomics. 2004, 84: 867-875. 10.1016/j.ygeno.2004.08.008.
Article
CAS
PubMed
Google Scholar
Yager TD, Dempsey AA, Tang H, Stamatiou D, Chao S, Marshall KW, Liew CC: First comprehensive mapping of cartilage transcripts to the human genome. Genomics. 2004, 84: 524-535. 10.1016/j.ygeno.2004.05.006.
Article
CAS
PubMed
Google Scholar
Vogel JH, von Heydebreck A, Purmann A, Sperling S: Chromosomal clustering of a human transcriptome reveals regulatory background. BMC Bioinformatics. 2005, 6: 230-10.1186/1471-2105-6-230.
Article
PubMed Central
PubMed
Google Scholar
Li Q, Lee BT, Zhang L: Genome-scale analysis of positional clustering of mouse testis-specific genes. BMC Genomics. 2005, 6: 7-10.1186/1471-2164-6-7.
Article
PubMed Central
PubMed
Google Scholar
Burhans DT, Ramachandran L, Wang J, Liang P, Patterton HG, Breitenbach M, Burhans WC: Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome. BMC Evol Biol. 2006, 6: 58-10.1186/1471-2148-6-58.
Article
PubMed Central
PubMed
Google Scholar
Lee JM, Sonnhammer EL: Genomic gene clustering analysis of pathways in eukaryotes. Genome Res. 2003, 13: 875-882. 10.1101/gr.737703.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fukuoka Y, Inaoka H, Kohane IS: Inter-species differences of co-expression of neighboring genes in eukaryotic genomes. BMC Genomics. 2004, 5: 4-10.1186/1471-2164-5-4.
Article
PubMed Central
PubMed
Google Scholar
Husing J, Zeschnigk M, Boes T, Jockel KH: Combining DNA expression with positional information to detect functional silencing of chromosomal regions. Bioinformatics. 2003, 19: 2335-2342. 10.1093/bioinformatics/btg314.
Article
PubMed
Google Scholar
Toedling J, Schmeier S, Heinig M, Georgi B, Roepcke S: MACAT--microarray chromosome analysis tool. Bioinformatics. 2005, 21: 2112-2113. 10.1093/bioinformatics/bti183.
Article
CAS
PubMed
Google Scholar
Zhou X, Cole SW, Rao NP, Cheng Z, Li Y, McBride J, Wong DT: Identification of discrete chromosomal deletion by binary recursive partitioning of microarray differential expression data. J Med Genet. 2005, 42: 416-419. 10.1136/jmg.2004.025353.
Article
CAS
PubMed Central
PubMed
Google Scholar
Zhou Y, Luoh SM, Zhang Y, Watanabe C, Wu TD, Ostland M, Wood WI, Zhang Z: Genome-wide identification of chromosomal regions of increased tumor expression by transcriptome analysis. Cancer Res. 2003, 63: 5781-5784.
CAS
PubMed
Google Scholar
Levin AM, Ghosh D, Cho KR, Kardia SL: A model-based scan statistic for identifying extreme chromosomal regions of gene expression in human tumors. Bioinformatics. 2005, 21: 2867-2874. 10.1093/bioinformatics/bti417.
Article
CAS
PubMed
Google Scholar
Crawley JJ, Furge KA: Identification of frequent cytogenetic aberrations in hepatocellular carcinoma using gene-expression microarray data. Genome Biol. 2002, 3: RESEARCH0075-10.1186/gb-2002-3-12-research0075.
Article
PubMed Central
PubMed
Google Scholar
Kano M, Nishimura K, Ishikawa S, Tsutsumi S, Hirota K, Hirose M, Aburatani H: Expression imbalance map: a new visualization method for detection of mRNA expression imbalance regions. Physiol Genomics. 2003, 13: 31-46.
Article
CAS
PubMed
Google Scholar
Callegaro A, Basso D, Bicciato S: A locally adaptive statistical procedure (LAP) to identify differentially expressed chromosomal regions. Bioinformatics. 2006, 22: 2658-2666. 10.1093/bioinformatics/btl455.
Article
CAS
PubMed
Google Scholar
Coppe A, Danieli GA, Bortoluzzi S: REEF: searching REgionally Enriched Features in genomes. BMC Bioinformatics. 2006, 7: 453-10.1186/1471-2105-7-453.
Article
PubMed Central
PubMed
Google Scholar
Reyal F, Stransky N, Bernard-Pierrot I, Vincent-Salomon A, de Rycke Y, Elvin P, Cassidy A, Graham A, Spraggon C, Desille Y, Fourquet A, Nos C, Pouillart P, Magdelenat H, Stoppa-Lyonnet D, Couturier J, Sigal-Zafrani B, Asselain B, Sastre-Garau X, Delattre O, Thiery JP, Radvanyi F: Visualizing chromosomes as transcriptome correlation maps: evidence of chromosomal domains containing co-expressed genes--a study of 130 invasive ductal breast carcinomas. Cancer Res. 2005, 65: 1376-1383. 10.1158/0008-5472.CAN-04-2706.
Article
CAS
PubMed
Google Scholar
Katsanis N, Worley KC, Gonzalez G, Ansley SJ, Lupski JR: A computational/functional genomics approach for the enrichment of the retinal transcriptome and the identification of positional candidate retinopathy genes. Proc Natl Acad Sci U S A. 2002, 99: 14326-14331. 10.1073/pnas.222409099.
Article
CAS
PubMed Central
PubMed
Google Scholar
Fujikado N, Saijo S, Iwakura Y: Identification of arthritis-related gene clusters by microarray analysis of two independent mouse models for rheumatoid arthritis. Arthritis Res Ther. 2006, 8: R100-
Article
PubMed Central
PubMed
Google Scholar
Zuckerkandl E: Sectorial gene repression in the control of development. Gene. 1999, 238: 263-276. 10.1016/S0378-1119(99)00293-0.
Article
CAS
PubMed
Google Scholar
Payne KJ, Crooks GM: Human hematopoietic lineage commitment. Immunol Rev. 2002, 187: 48-64. 10.1034/j.1600-065X.2002.18705.x.
Article
PubMed
Google Scholar
Metcalf D: The molecular control of cell division, differentiation commitment and maturation in haemopoietic cells. Nature. 1989, 339: 27-30. 10.1038/339027a0.
Article
CAS
PubMed
Google Scholar
Kondo M, Wagers AJ, Manz MG, Prohaska SS, Scherer DC, Beilhack GF, Shizuru JA, Weissman IL: Biology of hematopoietic stem cells and progenitors: implications for clinical application. Annu Rev Immunol. 2003, 21: 759-806. 10.1146/annurev.immunol.21.120601.141007.
Article
CAS
PubMed
Google Scholar
Georgopoulos K: Haematopoietic cell-fate decisions, chromatin regulation and ikaros. Nat Rev Immunol. 2002, 2: 162-174. 10.1038/nri747.
Article
CAS
PubMed
Google Scholar
Rosmarin AG, Yang Z, Resendes KK: Transcriptional regulation in myelopoiesis: Hematopoietic fate choice, myeloid differentiation, and leukemogenesis. Exp Hematol. 2005, 33: 131-143. 10.1016/j.exphem.2004.08.015.
Article
CAS
PubMed
Google Scholar
Orkin SH: Diversification of haematopoietic stem cells to specific lineages. Nat Rev Genet. 2000, 1: 57-64. 10.1038/35049577.
Article
CAS
PubMed
Google Scholar
Kluger Y, Lian Z, Zhang X, Newburger PE, Weissman SM: A panorama of lineage-specific transcription in hematopoiesis. Bioessays. 2004, 26: 1276-1287. 10.1002/bies.20144.
Article
CAS
PubMed
Google Scholar
Loose M, Patient R: Global genetic regulatory networks controlling hematopoietic cell fates. Curr Opin Hematol. 2006, 13: 229-236. 10.1097/01.moh.0000231419.15654.7f.
Article
CAS
PubMed
Google Scholar
Gemelli C, Montanari M, Tenedini E, Zanocco MT, Vignudelli T, Siena M, Zini R, Salati S, Tagliafico E, Manfredini R, Grande A, Ferrari S: Virally mediated MafB transduction induces the monocyte commitment of human CD34+ hematopoietic stem/progenitor cells. Cell Death Differ. 2006, 13: 1686-1696. 10.1038/sj.cdd.4401860.
Article
CAS
PubMed
Google Scholar
Chalifa-Caspi V, Yanai I, Ophir R, Rosen N, Shmoish M, Benjamin-Rodrig H, Shklar M, Stein TI, Shmueli O, Safran M, Lancet D: GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes. Bioinformatics. 2004, 20: 1457-1458. 10.1093/bioinformatics/bth081.
Article
CAS
PubMed
Google Scholar
Database for Annotation, Visualization and Integrated Discovery (DAVID) 2006. [http://niaid.abcc.ncifcrf.gov/]
Won KA, Schumacher RJ, Farr GW, Horwich AL, Reed SI: Maturation of human cyclin E requires the function of eukaryotic chaperonin CCT. Mol Cell Biol. 1998, 18: 7584-7589.
Article
CAS
PubMed Central
PubMed
Google Scholar
Calvo KR, Knoepfler PS, Sykes DB, Pasillas MP, Kamps MP: Meis1a suppresses differentiation by G-CSF and promotes proliferation by SCF: potential mechanisms of cooperativity with Hoxa9 in myeloid leukemia. Proc Natl Acad Sci U S A. 2001, 98: 13120-13125. 10.1073/pnas.231115398.
Article
CAS
PubMed Central
PubMed
Google Scholar
Spoelgen R, Hammes A, Anzenberger U, Zechner D, Andersen OM, Jerchow B, Willnow TE: LRP2/megalin is required for patterning of the ventral telencephalon. Development. 2005, 132: 405-414. 10.1242/dev.01580.
Article
CAS
PubMed
Google Scholar
Taylor A, Obholz K, Linden G, Sadiev S, Klaus S, Carlson KD: DNA sequence and muscle-specific expression of human sarcosin transcripts. Mol Cell Biochem. 1998, 183: 105-112. 10.1023/A:1006824331819.
Article
CAS
PubMed
Google Scholar
Qu S, Tucker SC, Zhao Q, deCrombrugghe B, Wisdom R: Physical and genetic interactions between Alx4 and Cart1. Development. 1999, 126: 359-369.
CAS
PubMed
Google Scholar
Li AH, Hwang HM, Tan PP, Wu T, Wang HL: Neurotensin excites periaqueductal gray neurons projecting to the rostral ventromedial medulla. J Neurophysiol. 2001, 85: 1479-1488.
CAS
PubMed
Google Scholar
Zhang Q, Fukuda M, Van Bockstaele E, Pascual O, Haydon PG: Synaptotagmin IV regulates glial glutamate release. Proc Natl Acad Sci U S A. 2004, 101: 9441-9446. 10.1073/pnas.0401960101.
Article
CAS
PubMed Central
PubMed
Google Scholar
Bamji SX, Shimazu K, Kimes N, Huelsken J, Birchmeier W, Lu B, Reichardt LF: Role of beta-catenin in synaptic vesicle localization and presynaptic assembly. Neuron. 2003, 40: 719-731. 10.1016/S0896-6273(03)00718-9.
Article
CAS
PubMed Central
PubMed
Google Scholar
Sagane K, Ohya Y, Hasegawa Y, Tanaka I: Metalloproteinase-like, disintegrin-like, cysteine-rich proteins MDC2 and MDC3: novel human cellular disintegrins highly expressed in the brain. Biochem J. 1998, 334 ( Pt 1): 93-98.
Article
CAS
Google Scholar
Golding JP, Trainor P, Krumlauf R, Gassmann M: Defects in pathfinding by cranial neural crest cells in mice lacking the neuregulin receptor ErbB4. Nat Cell Biol. 2000, 2: 103-109. 10.1038/35000058.
Article
CAS
PubMed
Google Scholar
Riccio A, Ahn S, Davenport CM, Blendy JA, Ginty DD: Mediation by a CREB family transcription factor of NGF-dependent survival of sympathetic neurons. Science. 1999, 286: 2358-2361. 10.1126/science.286.5448.2358.
Article
CAS
PubMed
Google Scholar
Teng J, Takei Y, Harada A, Nakata T, Chen J, Hirokawa N: Synergistic effects of MAP2 and MAP1B knockout in neuronal migration, dendritic outgrowth, and microtubule organization. J Cell Biol. 2001, 155: 65-76. 10.1083/jcb.200106025.
Article
CAS
PubMed Central
PubMed
Google Scholar
Kuppner MC, Gastpar R, Gelwer S, Nossner E, Ochmann O, Scharner A, Issels RD: The role of heat shock protein (hsp70) in dendritic cell maturation: hsp70 induces the maturation of immature dendritic cells but reduces DC differentiation from monocyte precursors. Eur J Immunol. 2001, 31: 1602-1609. 10.1002/1521-4141(200105)31:5<1602::AID-IMMU1602>3.0.CO;2-W.
Article
CAS
PubMed
Google Scholar
Kinet JP: The high-affinity IgE receptor (Fc epsilon RI): from physiology to pathology. Annu Rev Immunol. 1999, 17: 931-972. 10.1146/annurev.immunol.17.1.931.
Article
CAS
PubMed
Google Scholar
Kingsbury GA, Feeney LA, Nong Y, Calandra SA, Murphy CJ, Corcoran JM, Wang Y, Prabhu Das MR, Busfield SJ, Fraser CC, Villeval JL: Cloning, expression, and function of BLAME, a novel member of the CD2 family. J Immunol. 2001, 166: 5675-5680.
Article
CAS
PubMed
Google Scholar
Kruse M, Meinl E, Henning G, Kuhnt C, Berchtold S, Berger T, Schuler G, Steinkasserer A: Signaling lymphocytic activation molecule is expressed on mature CD83+ dendritic cells and is up-regulated by IL-1 beta. J Immunol. 2001, 167: 1989-1995.
Article
CAS
PubMed
Google Scholar
Morandi B, Costa R, Falco M, Parolini S, De Maria A, Ratto G, Mingari MC, Melioli G, Moretta A, Ferlazzo G: Distinctive lack of CD48 expression in subsets of human dendritic cells tunes NK cell activation. J Immunol. 2005, 175: 3690-3697.
Article
CAS
PubMed
Google Scholar
Martin M, Romero X, de la Fuente MA, Tovar V, Zapater N, Esplugues E, Pizcueta P, Bosch J, Engel P: CD84 functions as a homophilic adhesion molecule and enhances IFN-gamma secretion: adhesion is mediated by Ig-like domain 1. J Immunol. 2001, 167: 3668-3676.
Article
CAS
PubMed
Google Scholar
Romero X, Benitez D, March S, Vilella R, Miralpeix M, Engel P: Differential expression of SAP and EAT-2-binding leukocyte cell-surface molecules CD84, CD150 (SLAM), CD229 (Ly9) and CD244 (2B4). Tissue Antigens. 2004, 64: 132-144. 10.1111/j.1399-0039.2004.00247.x.
Article
CAS
PubMed
Google Scholar
Montanari M, Gemelli C, Tenedini E, Zanocco MT, Vignudelli T, Siena M, Zini R, Salati S, Chiossi G, Tagliafico E, Manfredini R, Grande A, Ferrari S: Correlation between differentiation plasticity and mRNA expression profiling of CD34+- derived CD14- and CD14+ human normal myeloid precursors. Cell Death Differ. 2005, 12 (12): 1588-600. 10.1038/sj.cdd.4401679.
Article
CAS
PubMed
Google Scholar
Tenedini E, Fagioli ME, Vianelli N, Tazzari PL, Ricci F, Tagliafico E, Ricci P, Gugliotta L, Martinelli G, Tura S, Baccarani M, Ferrari S, Catani L: Gene expression profiling of normal and malignant CD34-derived megakaryocytic cells. Blood. 2004, 104: 3126-3135. 10.1182/blood-2003-07-2597.
Article
CAS
PubMed
Google Scholar
Grande A, Piovani B, Aiuti A, Ottolenghi S, Mavilio F, Ferrari G: Transcriptional targeting of retroviral vectors to the erythroblastic progeny of transduced hematopoietic stem cells. Blood. 1999, 93: 3276-3285.
CAS
PubMed
Google Scholar
Draghici S, Khatri P, Eklund AC, Szallasi Z: Reliability and reproducibility issues in DNA microarray measurements. Trends Genet. 2006, 22: 101-109. 10.1016/j.tig.2005.12.005.
Article
CAS
PubMed Central
PubMed
Google Scholar
Shi L, Reid LH, Jones WD, Shippy R, Warrington JA, Baker SC, Collins PJ, de Longueville F, Kawasaki ES, Lee KY, Luo Y, Sun YA, Willey JM, Setterquist RA, Fischer GM, Tong W, Dragan YP, Dix DJ, Frueh FW, Goodsaid FM, Herman D, Jensen RV, Johnson CD, Lobenhofer EK, Puri RK, Schrf U, Thierry-Mieg J, Wang C, Wilson M, Wolber PK, Zhang L, Slikker W, Shi L, Reid LH: The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol. 2006, 24: 1151-1161. 10.1038/nbt1239.
Article
CAS
PubMed
Google Scholar
Mecham BH, Wetmore DZ, Szallasi Z, Sadovsky Y, Kohane I, Mariani TJ: Increased measurement accuracy for sequence-verified microarray probes. Physiol Genomics. 2004, 18: 308-315. 10.1152/physiolgenomics.00066.2004.
Article
CAS
PubMed
Google Scholar
Grande A, Montanari M, Tagliafico E, Manfredini R, Marani TZ, Siena M, Tenedini E, Gallinelli A, Ferrari S: Physiological levels of 1alpha, 25 dihydroxyvitamin D3 induce the monocytic commitment of CD34+ hematopoietic progenitors. J Leukoc Biol. 2002, 71: 641-651.
CAS
PubMed
Google Scholar
Manfredini R, Zini R, Salati S, Siena M, Tenedini E, Tagliafico E, Montanari M, Zanocco-Marani T, Gemelli C, Vignudelli T, Grande A, Fogli M, Rossi L, Fagioli ME, Catani L, Lemoli RM, Ferrari S: The kinetic status of hematopoietic stem cell subpopulations underlies a differential expression of genes involved in self-renewal, commitment, and engraftment. Stem Cells. 2005, 23: 496-506. 10.1634/stemcells.2004-0265.
Article
CAS
PubMed
Google Scholar
Guglielmelli P, Zini R, Bogani C, Salati S, Pancrazzi A, Bianchi E, Mannelli F, Ferrari S, Le Bousse-Kerdiles MC, Bosi A, Barosi G, Migliaccio AR, Manfredini R, Vannucchi AM: Molecular profiling of CD34+ cells in idiopathic myelofibrosis identifies a set of disease-associated genes and reveals the clinical significance of Wilm's tumor gene (WT1). Stem Cells. 2007 Jan;25(1):165-73. 2006, 25 (1): 165-73.
Google Scholar
Stegmaier K, Ross KN, Colavito SA, O'Malley S, Stockwell BR, Golub TR: Gene expression-based high-throughput screening(GE-HTS) and application to leukemia differentiation. Nat Genet. 2004, 36: 257-263. 10.1038/ng1305.
Article
CAS
PubMed
Google Scholar
Data repository at the eXperimental genomics & transcriptomics Laboratory web site. [http://www.xlab.unimo.it/XLab/ExpDataView.php]
GeneALaCart. [http://www.genecards.org/BatchQueries/]
Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001, 98: 5116-5121. 10.1073/pnas.091062498.
Article
CAS
PubMed Central
PubMed
Google Scholar
GOHyperGAll. [http://www.geneontology.org/GO.tools.microarray.shtml#GOHyperGAll]