Bioinformatics of transcriptome analysis in cancer biology;Analyse du transcriptome en cancérologie: Aspects bio-informatiques

Bulletin du Cancer

Volumn 88, Issue 3, 2001, Pages 269-276

  Claverie, J M ^a  

^a CNRS Aix Marseille University   (France)

Author keywords

Bioinformatics; Microarray; Transcriptome

Indexed keywords

CANCER; CANCER DIAGNOSIS; CELL CULTURE; DIAGNOSTIC VALUE; DISEASE CLASSIFICATION; DNA MICROARRAY; GENE EXPRESSION; HUMAN; IN VITRO STUDY; PREDICTION; PROGNOSIS; REVIEW; TRANSCRIPTION REGULATION; CLASSIFICATION; FORECASTING; GENE EXPRESSION PROFILING; GENETICS; NEOPLASM;

FORECASTING; GENE EXPRESSION PROFILING; HUMANS; NEOPLASMS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS;

EID: 0034744655     PISSN: 00074551     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (96)

1. The sequence of the human genome
2. The genome sequence of Drosophila melanogaster
3. Genome sequence of the nematode C. elegans: A platform for investigating biology
4. Status of genome projects for nonpathogenic bacteria and archaea
5. The Pfam protein families database
6. New opportunities for uncovering the molecular basis of cancer
7. Expression profiling using cDNA microarrays
8. Exploring the new world of the genome with DNA microarrays
9. DNA microarrays in drug discovery and development
10. Gene expression informatics - It's all in your mine
11. Microarrays: Biotechnology's discovery platform for functional genomics
12. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression
13. Sequence identification of 2,375 human brain genes
14. Identification of new genes by systematic analysis of cDNAs and database construction
15. Generation and analysis of 280,000 human expressed sequence tags
16. Alternate polyadenylation in human mRNAs: A large-scale analysis by EST clustering
17. BodyMap: A collection of 3′ ESTs for analysis of human gene expression information
18. Serial analysis of gene expression
19. SAGEmap: A public gene expression resource
20. Developmental kinetics of GAD family mRNAs parallel neurogenesis in the rat spinal cord
21. A method for analyzing the qualitative and quantitative aspects of gene expression: A transcriptional profile revealed for HeLa cells
22. Quantitative monitoring of gene expression patterns with a complementary DNA microarray
23. Use of a cDNA microarray to analyse gene expression patterns in human cancer
24. Exploring the metabolic and genetic control of gene expression on a genomic scale
25. Genomics and array technology
26. Lightdirected, spatially addressable parallel chemical synthesis
27. High density synthetic oligonucleotide arrays
28. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays
29. The significance of digital gene expression profiles
30. Computational methods for the identification of differential and coordinated gene expression
31. Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis
32. An expressed-sequence-tag database of the human prostate: Sequence analysis of 1,168 cDNA clones
33. Gene expression profiles in normal and cancer cells
34. Sage transcript profiles for p53-dependent growth regulation
35. Identification of c-MYC as a target of the APC pathway
36. Serial analysis of gene expression in non-small cell lung cancer
37. Quantitative monitoring of gene expression patterns with a complementary DNA microarray
38. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization
39. On the analysis of the ratio of two correlated normal variables
40. The probability distribution of the ratio of the absolute values of two normal variables
41. The distribution of the ratio of two variables
42. Ratio-based decisions and the quantitative analysis of cDNA microarray images
43. Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations
44. Tissue gene expression analysis using arrayed normalized cDNA libraries
45. Normalization strategies for cDNA microarrays
46. Identification by cDNA microarray of genes involved in ovarian carcinogenesis
47. Identification of differentially expressed genes in nasopharryngeal carcinoma by means of the Atlas human cancer cDNA expression array
48. Identification of differentially expressed genes in human prostate cancer using subtraction and microarray
49. Microarray-based expression profiling in prostate tumors
50. Identification of genes differentially over-expressed in lung squamous cell carcinoma using combination of cDNA subtraction and microarray analysis
51. Genomic analysis of metastasis reveals an essential role for RhoC
52. Analysis of p53-regulated gene expression patterns using oligonucleotide arrays
53. Systematic variation in gene expression patterns in human cancer cell lines
54. Adult T-cell leukemia cells over-express the multidrug-resistance-protein (MRP) and lung-resistance-protein (LRP) genes
55. Transactivation of the multidrug resistance 1 gene by T-cell factor 4/beta-catenin complex in early colorectal carcinogenesis
56. EGR1 target genes in prostate carcinoma cells identified by microarray analysis
57. Differentially expressed genes in two LNCaP prostate cancer cell lines reflecting changes during prostate cancer progression
58. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays
59. The transcriptional program in the response of human fibroblast to serum
60. Drug target validation and identification of secondary drug target effects using DNA microarrays
61. Monitoring the expression profiles of doxorubicin-induced and doxorubicin-resistant cancer cells by cDNA microarray
62. Use of cDNA microarrays to probe and understand the toxicological consequences of altered gene expression
63. A gene expression database for the molecular pharmacology of cancer
64. Cluster analysis and data visualization of large-scale gene expression data
65. Large-scale temporal gene expression mapping of central nervous system development
66. Cluster analysis and display of genome-wide expression patterns
67. Computational aspects of expression data
68. Data management and analysis for gene expression arrays
69. Mutual information relevance networks: Functional genomic clustering using pairwise entropy measurements
70. Multivariate measurement of gene expression relationships
71. Singular value decomposition for genome-wide expression data processing and modeling
72. Phylip-Phylogeny inference package
73. Gene expression data analysis
74. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation
75. Gene expression profiling of alveolar rhabdomyosarcoma with cDNA microarrays
76. Application of comparative genomic hybridization, spectral karyotyping, and microarray analysis in the identification of subtype-specific patterns of genomic changes in rhabdomyosarcoma
77. Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring
78. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling
79. Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas
80. Molecular classification of cutaneous malignant melanoma by gene expression profiling
81. Molecular portraits of human breast tumours
82. Linking gene expression patterns to therapeutic groups in breast cancer
83. Hormone therapy failure in human prostate cancer: Analysis by cDNA and tissue microarrays
84. Genetic instability in colorectal cancers
85. Genetic instability of cancer cells is proportional to their degree of aneuploidy
86. Significance of multiple mutations in cancer
87. Gene expression profiles of hereditary breast cancer
88. A measure of progress in fold recognition?
89. DNA arrays for analysis of gene expression
90. Genomics and array technology