Dataset Information

Log-odds sequence logos.

ABSTRACT: MOTIVATION:DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns. RESULTS:We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column's observations are better explained as arising from relatedness or chance. Within this framework, we propose distinct normalized maximum likelihood and Bayesian measures of column information. We illustrate these measures on High Mobility Group B (HMGB) box proteins and a dataset of enzyme alignments. Particularly in the context of protein alignments, our measures improve the discrimination of biologically relevant positions. AVAILABILITY AND IMPLEMENTATION:Our new measures are implemented in an open-source Web-based logo generation program, which is available at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/logoddslogo/index.html. A stand-alone version of the program is also available from this site. CONTACT:altschul@ncbi.nlm.nih.gov SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Yu YK

PROVIDER: S-EPMC4318935 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

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Log-odds sequence logos.

Yu Yi-Kuo YK Capra John A JA Stojmirović Aleksandar A Landsman David D Altschul Stephen F SF

Bioinformatics (Oxford, England) 20141006 3

<h4>Motivation</h4>DNA and protein patterns are usefully represented by sequence logos. However, the methods for logo generation in common use lack a proper statistical basis, and are non-optimal for recognizing functionally relevant alignment columns.<h4>Results</h4>We redefine the information at a logo position as a per-observation multiple alignment log-odds score. Such scores are positive or negative, depending on whether a column's observations are better explained as arising from relatedne ...[more]

PMID: 25294922

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Project description:BACKGROUND:Globally, colorectal cancer (CRC) is the third and second leading cancer in men and women respectively with 600,000 deaths per year. Traditionally, clinicians have relied solely on nodal disease involvement, and measurements such as lymph node ratio (LNR; the ratio of metastatic/positive lymph nodes to total number of lymph nodes examined), when determining patient prognosis in CRC. The log odds of positive lymph nodes (LODDS) is a logistic transformation formula that uses pathologic lymph node data to stratify survival differences among patients within a single stage of disease. This formula allows clinicians to identify whether patients with clinically aggressive tumours fall into higher-risk groups regardless of nodal positivity and can potentially guide adjuvant treatment modalities. The aim of this study was to investigate whether LODDS in colon cancer provides better prognostication compared to LNR. METHODS:A retrospective study of patients on the prospectively maintained Cabrini Monash University Department of Surgery colorectal neoplasia database, incorporating data from hospitals in Melbourne Australia, identified patients entered between January 2010 and March 2016. Association of LODDS and LNR with clinical variables were analysed. Disease-free (DFS) and overall (OS) survival were investigated with Cox regression and Kaplan-Meier survival analyses. RESULTS:There were 862 treatment episodes identified in the database (402 male, 47%). The median patient age was 73 (range 22-100?years). There were 799 colonic cancers and 63 rectosigmoid cancers. The lymph node yield (LNY) was suboptimal (<?12) in 168 patients (19.5%) (p?=?0.05). The 5-year OS for the different LNR groups were 86, 91 and 61% (p?<?0.001) for LNR0 (655 episodes), LNR1 (128 episodes) and LNR2 (78 episodes), respectively. For LODDS, they were 85, 91 and 61% (p?<?0.001) in LODDS0 (569 episodes), LODDS1 (217 episodes) and LODDS2 (75 episodes) groups (p?<?0.001). Overall survival rates were comparable between the LNR and LODDS group and for LNY?<?12 and stage III patients when each were sub-grouped by LODDS and LNR. CONCLUSION:This study has shown for that the prognostic impact of LODDS is comparable to LNR for colon cancer patients. Accordingly, LNR is recommended for prognostication given its ease of calculation.

Dataset Information

Log-odds sequence logos.

Publications

Log-odds sequence logos.

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