My functional genomics and data mining glossaries

Here I will provide the links to definition and detail examples if available of some common terms that will be used in functional genomics, microarray & analysis, bioinformatics, proteomics, complex disease mapping & linkage analysis. The emphasis will be on the statistical ideas or mathematical models that used to analyse the data which usually not explain explicitly in papers. Please suggest your term/ report outdated links to me.

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z | other

*The format of glossaries is

term - link 1, link2a, link 2b,

where individual numbers donate different sites while alphabets link to continuous pages of the same term under the same site.

# The first links for each term will be those with simple definition while the followings will contain thorough discussion, text and examples.

# If you are looking for papers for a particular area like clustering for microarray, please refer to My functional genomics journal watch.

Can't find the glossaries you want in my site? Try a Google search!

A

ANCOVA (analysis of covariance) - link 1; link 2;
Anderson-Darling Test - link 1;
ANOVA (analysis of variance) - link 1; link 2;
ANOVA, one-way - link 1;
ANOVA, two-way - link 1;
Average linkage clustering - link 1;

B

Bayesian approach - link 1; link 2;
Bayesian logic - link 1;
Bayesian network - link 1;
Bayesian statistics - pdf;
Bayesian Theorem - link 1;
Bioformatics - link 1;
Bonferroni adjustment procedure - link 1;
Bootstrapping - link 1;link 2;link 3; link 4;

C

Case controlled study - link 1;
Chi-square Test - link 1;link 2; link 3; link 4;link 5(a web calculator for 2 by 2 chi square test);
Chi-square distribution - link 1;
City block distance (Manhattan distance) - link 1;
Cluster analysis - link 1; link 2; link 3; link 4; link 5;
Clustering algorithms - link 1; link 2;
Clustering, average linkage - link 1;
Clustering, complete linkage (Furthest Neighbour) - link 1;
Clustering, single linkage (Nearest Neighbour) - link 1;
Coefficient of Determination (R²) - link 1; link 2; link 3; link 4;
Coefficient of variation - link 1;
Combination (probability) - link 1;
Comparative Genomics - link 1;
Complete linkage clustering (Furthest Neighbour) - link 1;
Confidence Intervals - link 1;
Correlation - link 1; link 2; link 3;
Correlation coefficient - link 1;
Cross sectional studies - link 1;

D

Degree of freedom - link 1;
Dendrogram - link 1;
Distance measure - link 1;

E

Eigenvalues - link 1; link 2; link 3a; link 3b; link 3c; link 4; link 5;
Eigenvectors - link 1; link 2; link 3a; link 3b; link 3c; link 4; link 5;
Epistasis - link 1;
Euclidean distance - link 1

F

F-distribution - link 1;
F-test - link 1;
Factor analysis - link 1;
Forward genetics - link 1;
Furthest Neighbour clustering (Complete linkage) -link 1;
Functional Genomics - link 1;

G

Gaussian distribution (Normal distribution) - link 1; link 2;
Genome - link 1;
Genomics - link 1; link 2;

H

Hardy-Weinberg Equilibrum - link 1;link 2;
Hidden Markov Model - link 1; link 2;
Hierarchical clustering - link 1;

K

K-means Clustering - link 1;
Kolmogorov-Smirnov Goodness-of-Fit Test - link 1;
Kurtosis - link 1; link 2;link 3;

L

Linkage, genetic - link 1; link 2;
Linkage disequilibrium - link 1; link 2;
Loess - link 1; link 2;
Logistic Regression - link 1; link 2; link 3;link 4; link 5;
Lowess - link 1;

M

Manhattan distance (City block distance) - link 1;
Mann-Whitney (Wilcoxon Rank-Sum) test - link 1; link 2; link 3;
MANOVA (Multivariate analysis of variance) - link 1;
MANCOVA - link 1;
Markov Chain - link 1;
Matrix - link 1;link 2; link 3;
Matrix, orthogonal - link 1;
Mean, arithmetic - link 1
Mean, geometric - link 1;
Median - link 1
Mode - link 1
Multidimensional Scaling (MDS) - link 1; link2;
Multiple hypothesis testing - link 1; link 2;
Multiple regression - link 1;
Multivariate statistical techniques - link 1;
Multivariate statistical techniques, regression type - link 1;
Multivariate statistical techniques, ordination type - link 1;

N

Nearest Neighbour Clustering (Single linkage) - link 1;
Non-Parametric Statistical Methods - link 1;
Normal distribution (Gaussian distribution) - link 1; link2;link 3;

P

Pearson's Correlation Coefficient - link 1; link 2; link 3; link 4; link 5; link 6;
Perceptrons - link 1;
Permutation - link 1; link 2; link 3;
Phenocopy - link 1;
Pleiotropy - link 1;
Poisson distribution - link 1;link 2
Principal component analysis (PCA) - link 1a; link 1b; link 1c; [link 2: ps, word];

Q

Quantile - link 1;
Quantile-Quantile (Q-Q) plot - link 1; link 2;

R

Regression analysis - link 1;
Reverse genetics - link 1; link2;link 3;
Root mean square - link 1; link 2;

S

Self-Organizing Map (SOM; Kohonen's Self-Organizing Map) - link 1; link 2; link 3;
Set (mathematics) - link 1;
Shapiro-Wilk Test - link 1;
Signum Function - link 1; link 2;
Single linkage Clustering (Nearest Neighbour) - link 1;
Singular Value Decomposition (SVD) - link 1; link 2;link 3;
Skewness - link 1;link 2;
Spearman's Rank Correlation - link 1;
Standard deviation - link 1;link 2;
Standard error - link 1;
Standard normal distribution - link 1;
Standard score (Z score) - link 1;link 2;
Stem cells, totipotent - link 1;
Stem cells, pluripotent - link 1;
Stem cells, multipotent - link 1;
Support vector machines (SVMs) - link 1a; link 1b; link 2;
Symbols, mathematical - link 1; link 2;
System Biology - link 1;link 2;

T

t-distribtuion - link 1; link 2;
t-test - link 1;
t-test, independent group - link 1;
t-test, paired sample - link 1; link 2;
t-test, single sample - link 1;
t-test, student's - link 1;link 2;
Tramission disequilibrium test (TDT) - link 1;
Type I & Type II error - link 1;

U

UPGMA (Unweighted Pair Group Method with Arithmatic Mean) - link 1;link 2; link 3;
WPGMA (Weighted Pair Group Method with Arithmatic Mean) - link 1;

V

Variance - link 1; link 2s

W

Wilcoxon Rank-Sum (Mann-Whitney) Test - link 1; link 2; link 3;

Z

Z score (standard score) - link 1;link 2;

last updated: 12 Jan 2004
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