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Several over-represented eight-letter words have known biological functions described in the eukaryotic transcription factor database TRANSFAC; however, many did not.

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research 32 (3), 2004

Besides calculating a P -value with the standard normal approximation associated with z -scores, we used two extra statistical controls to evaluate the significance of over-represented words.

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research 32 (3), 2004

These controls have important implications for evaluating over- and under-represented words with z -scores.

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research 32 (3), 2004

These elements can be identified by enumerative methods, which count all possible DNA words of a certain length in promoter sequences and then use statistics such as z -scores to evaluate over-represented words ( 13 – 16 ).

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research 32 (3), 2004

Here we describe the results of applying enumerative methods to eight-letter words in the human PPRs where the statistical significance of over-represented words was determined using three different methods: (i) analytically derived z -scores (the standard method of assigning statistical significances to exact word matches in DNA); (ii) computer simulation of the Markov chain underlying the z -scores, to compare the z -scores with the actual extreme value distribution that they are supposed to approximate; and (iii) computer simulation of 1000 mock data sets, composed of matched, uniform random DNA sequences from the human genome (which produced P -values that were much more conservative than the z -scores).

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research 32 (3), 2004

1307 further examples >>
Publications
 

Statistical analysis of over-represented words in human promoter sequences

Leonardo Mariño-Ramírez et al.

Nucleic Acids Research , 2004

An approach to identify over-represented cis -elements in related sequences

Jiashun Zheng et al.

Nucleic Acids Research , 01 Apr 2003

Ibuprofen 400 mg is effective in women, and women are well represented in trials

Jodie Barden et al.

BMC Anesthesiology , 01 Nov 2002

Reproducibility of dynamically represented acoustic lung images from healthy individuals

T M Maher et al.

Thorax , 01 Jun 2008

Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes.

B Shomer et al.

Nucleic Acids Research , 15 Nov 1999

Putative Zinc Finger Protein Binding Sites Are Over-Represented in the Boundaries of Methylation-Resistant CpG Islands in the Human Genome

Shicai Fan et al.

PLoS ONE , 21 Nov 2007

oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes

Shannan J. Ho Sui et al.

Nucleic Acids Research , 2005

How to decide which are the most pertinent overly-represented features during gene set enrichment analysis

Roland Barriot et al.

BMC Bioinformatics , 11 Sep 2007

SLiMFinder: A Probabilistic Method for Identifying Over-Represented, Convergently Evolved, Short Linear Motifs in Proteins

Richard J. Edwards et al.

PLoS ONE , 03 Oct 2007

A systematic review of how homeopathy is represented in conventional and CAM peer reviewed journals

Timothy Caulfield et al.

BMC Complementary and Alternative Medicine , 14 Jun 2005

1302 further publications >>