Bioinformatics and Functional Genomics

Table 6-1. Histogram of cluster sizes for human entries in UniGene (build 153, Homo sapiens)(http://www.ncbi.nlm.nih.gov/UniGene/Hs.stats.shtml).

Cluster size	Number of clusters
1	36206
2	14384
3-4	15804
5-8	10612
9-16	5852
17-32	3986
33-64	3516
65-128	4095
129-256	3953
257-512	2170
513-1024	709
1025-2048	213
2049-4096	70
4097-8192	26
8193-16384	5
16385-32768	1

 

Table 6-3. Fisher's 2 x 2 Exact Test is used to test the null hypothesis that a given gene (gene 1) is not differentially regulated in two pools. Adapted from Claverie (1999) and http://www.ncbi.nlm.nih.gov/UniGene/fisher.shtml.

	Gene 1	All other genes	Total
Pool A (e.g. brain)	Number of sequences assigned to gene 1 (g1A)	Number of sequences in this pool NOT gene 1 (NA – g1A)	NA
Pool B (e.g. muscle)	Number of sequences assigned to gene 1 (g1B)	Number of sequences in this pool NOT gene 1 (NB – g1B)	NB
Total	c = g1A + g1B	C = (NA – g1A) + (NB – g1B)

 

Table 6-4. Major advantages of microarray experiments.

Advantage	Comment
Fast	One can obtain data on the expression of >10,000 genes with one week
Comprehensive	The entire yeast genome can be represented on a chip
Flexible	cDNAs or oligonucleotides corresponding to any gene can be represented on a chip

 

Table 6-5. Major disadvantages of microarray experiments.

Disadvantage	Comment
Cost	Many researchers find it prohibitively expensive to perform sufficient replicates and other controls.
Unknown significance of RNA	The final product of gene expression is protein, not RNA
Uncertain quality control	It is impossible for most investigators to assess the identity of DNA immobilized on any microarray. Also, there are many artifacts associated with image analysis and data analysis.

 

Table 6-6. Repositories for microarray data.

Repository	Comment
AMAD	From Stanford and the University of California at Berkeley and at San Francisco
ArrayExpress	From Alvis Brazma and colleagues at the EBI
ChipDB	From the Whitehead Institute
ExpressDB	At Harvard; relational database containing yeast RNA expression data.
GeneDirector	From Biodiscovery
GeNet	From Silicon Genetics
GeneX	From NCGR
GEO	Gene Expression Omnibus from NCBI
GXD	From the Jackson Laboratory
MAdb	National Cancer Institute
MaxdSQL	The University of Manchester
RAD	U. Pennsylvania
Stanford Microarray Database	Stanford University