Estimating mutual information using B-spline functions - An improved similarity measure for analysing gene expression data

BMC Bioinformatics

Volumn 5, Issue , 2004, Pages

  Daub, Carsten O ^a,d   Steuer, Ralf ^b   Selbig, Joachim ^a   Kloska, Sebastian ^a,c  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b UNIVERSITY OF POTSDAM   (Germany)

^c SCIENION AG   (Germany)

^d KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTERISTIC PROPERTIES; GENE EXPRESSION DATA; GENE EXPRESSION DATASETS; MUTUAL INFORMATIONS; NON-LINEAR CORRELATIONS; NUMERICAL ESTIMATION; RANDOM CORRELATIONS; SIMILARITY MEASURE;

ALGORITHMS; INTERPOLATION;

GENE EXPRESSION;

ACCESS TO INFORMATION; ALGORITHM; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION; GENETIC SIMILARITY; INFORMATION PROCESSING; INTERMETHOD COMPARISON; INTERNET; LINEAR SYSTEM; NONLINEAR SYSTEM; RANDOMIZATION; STATISTICAL PARAMETERS; STATISTICAL SIGNIFICANCE; BIOLOGY; COMPARATIVE STUDY; DNA MICROARRAY; FUZZY LOGIC; GENE EXPRESSION PROFILING; INFORMATION SCIENCE; PROCEDURES; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; FUZZY LOGIC; GENE EXPRESSION PROFILING; INFORMATION SCIENCE; MODELS, THEORETICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 13244267007     PISSN: 14712105     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2105-5-118     Document Type: Article

References (33)

1. Schena M, Shalon D, Davis RW, Brown PO: Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray. Science 1995, 270:467-470.
2. Velculescu VE, Zhang I, Vogelstein B, Kinzler K: Serial Analysis of Gene Expression. Science 1995, 270:484-487.
3. Eisen MB, Spellman PT, Brown PO, Botstein D: Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998, 95:14863-14868.
4. D'haeseleer P, Weng X, Fuhrman S, Somogyi R: Information processing in cells and tissues. Plenum Publishing 1997:203-212 [http://www.cs.unm.edu/~patrik/networks/IPCAT/ipcat.html].
5. D'haeseleer P, Liang S, Somogyi R: Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 2000, 16:707-726.
6. Michaels GS, Carr DB, Askenazi M, Fuhrmann S, Wen X, Somogyi R: Cluster analysis and data visualization of large-scale gene expression data. Pac Symp Biocomput 1998:42-53.
7. Butte AJ, Kohane IS: Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements. Pac Symp Biocomput 2000, 5:427-439.
8. Herwig R, Poustka AJ, Muller C, Bull C, Lehrach H, O'brien J: Large-scale clustering of cDNA-fingerprinting data. Genome Res 1999, 9:1093-1105.
9. Korber BT, Farber RM, Wolpert DH, Lapedes AS: Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis. Proc Natl Acad Sci USA 1993, 90:7176-7180.
10. Gorodkin J, Heyer LJ, Brunak S, Stormo GD, Wen X, Somogyi R: Display the information contents of structural RNA alignments: the structure logos. Comput Appl Biosci 1997, 13:583-586.
11. Liang S, Fuhrman S, Somogyi R: Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac Symp Biocomput 1998:18-29.
12. Roberts S, Everson R: Independent component analysis: Priciples and Practice. Cambridge: Cambridge University Press; 2001.
13. Hyvärinen A, Karhunne J, Oja E: Independent component analysis. New York: Wiley; 2001.
14. Fraser AM, Swinney HL: Independent coordinates for strange attractors from mutual information. Phys Rev A 1986, 33: 318-2321.
15. Thénevaz P, Unser M: Optimization of mutual information for multiresolution image registration. IEEE Trans Image Processing 2000, 9:2083-2099.
16. Ellis DP, Bilmes JA: Using mutual information to design feature combinations. In Proceedings of the International Conference on Spoken Language Processing: Beijing [http://www.icsi.berkeley.edu/ftp/global/pub/speech/papers /icslp00-cmi.pdf]. 16-20 October 2000
17. Shannon CE: A mathematical theory of communication. The Bell System Technical Journal 1948,27:623-656.
18. Moon Y, Rajagopalan B, Lall U: Estimation of mutual information using kernel density estimators. Phys Rev E 1995, 52:2318-2321.
19. Silverman BW: Density estimation for statistics and data analysis. London: Chapman and Hall; 1986.
20. Steuer R, Kurths J, Daub CO, Weise J, Selbig J: The mutual information: detecting end evaluating dependencies between variables. Bioinformatics 2002:S231-S240.
21. Paninski L: Estimation of Entropy and Mutual Information. Neural Computation 2003, 15:1191-1253.
22. DeBoor C: A practical guide to splines. New York: Springer; 1978.
23. Unser M, Aldroubi A, Eden M: B-spline signal processing: Part 1 - Theory. IEEE Trans Signal Precessing 1993, 41: 21-832.
24. Unser M, Aldroubi A, Eden M: B-spline signal processing: Part 2 - Efficient design and applications. IEEE Trans Signal Precessing 1993, 41:834-848.
25. Herzel H, Schmidt AO, Ebeling W: Finite sample effects in sequence analysis. Chaos, Solitons & Fractals 1994, 4: 7-113.
26. Herzel H, Grosse I: Measuring correlations in symbol sequences. Physica A 1995, 216:518-542.
27. Grosse I: Estimating entropies from finite samples. In Dynamik, Evolution, Strukturen Edited by: Freund JA. Berlin: Dr. Köster; 1996:181-190.
28. Roulston MS: Estimating the error on measured entropy and mutual information. Physica D 1999, 125:285-294.
29. Herzel H, Grosse I: Correlations in DNA sequences: The role of protein coding segments. Phy Rev E 1997, 55: 00-810.
30. Klus GT, Song A, Schick A, Wahde M, Szallasi Z: Mutual Information Analysis as a Tool to Assess the Role of Aneuploidy in the Generation of Cancer-Associated Differential Gene Expression Patterns. Pac Symp Biocomput 2001:42-51.
31. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey HA, Dai H, He YD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH: Functional Discovery via a Compendium of Expression Profiles. Cell 2000, 102:109-126.
32. Steuer R, Daub CO, Selbig J, Kurths J: Measuring distances between variables by mutual information. In Proceedings of the 27th Annual Conference of the Gesellschaft für Klassifikation: Cottbus in press. 12-14 March 2003
33. He YD, Dai H, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB: Microarray standard data set and figures of merit for comparing data processing methods and experiment design. Bioinformatics 2003, 19:956-965.