Data Discovery and Anomaly Detection Using Atypicality: Theory

A central question in the era of 'big data' is what to do with the enormous amount of information. One possibility is to characterize it through statistics, e.g., averages, or classify it using machine learning, in order to understand the general structure of the overall data. The perspective in this paper is the opposite, namely that most of the value in the information in some applications is in the parts that deviate from the average, that are unusual, atypical. We define what we mean by 'atypical' in an axiomatic way as data that can be encoded with fewer bits in itself rather than using the code for the typical data. We show that this definition has good theoretical properties. We then develop an implementation based on universal source coding, and apply this to a number of real world data sets.Comment: 40 page

Breast Cancer Patient Data from TCGA.

<p>Breast Cancer Patient Data from TCGA.</p

Elevated Resistin Gene Expression in African American Estrogen and Progesterone Receptor Negative Breast Cancer

<div><p>Introduction</p><p>African American (AA) women diagnosed with breast cancer are more likely to have aggressive subtypes. Investigating differentially expressed genes between patient populations may help explain racial health disparities. Resistin, one such gene, is linked to inflammation, obesity, and breast cancer risk. Previous studies indicated that resistin expression is higher in serum and tissue of AA breast cancer patients compared to Caucasian American (CA) patients. However, resistin expression levels have not been compared between AA and CA patients in a stage- and subtype-specific context. Breast cancer prognosis and treatments vary by subtype. This work investigates differential resistin gene expression in human breast cancer tissues of specific stages, receptor subtypes, and menopause statuses in AA and CA women.</p><p>Methods</p><p>Differential gene expression analysis was performed using human breast cancer gene expression data from The Cancer Genome Atlas. We performed inter-race resistin gene expression level comparisons looking at receptor status and stage-specific data between AA and CA samples. DESeq was run to test for differentially expressed resistin values.</p><p>Results</p><p>Resistin RNA was higher in AA women overall, with highest values in receptor negative subtypes. Estrogen-, progesterone-, and human epidermal growth factor receptor 2- negative groups showed statistically significant elevated resistin levels in Stage I and II AA women compared to CA women. In inter-racial comparisons, AA women had significantly higher levels of resistin regardless of menopause status. In whole population comparisons, resistin expression was higher among Stage I and III estrogen receptor negative cases. In comparisons of molecular subtypes, resistin levels were significant higher in triple negative than in luminal A breast cancer.</p><p>Conclusion</p><p>Resistin gene expression levels were significantly higher in receptor negative subtypes, especially estrogen receptor negative cases in AA women. Resistin may serve as an early breast cancer biomarker and possible therapeutic target for AA breast cancer.</p></div

Inter-racial comparison of resistin gene expression between Caucasian American and African American breast tumors by stage/menopause status.

<p>Inter-racial comparison of resistin gene expression between Caucasian American and African American breast tumors by stage/menopause status.</p

Resistin gene expression in whole population breast tumors by stage and receptor status.

<p>Resistin gene expression in whole population breast tumors by stage and receptor status.</p

Intra-racial comparison of resistin gene expression of Caucasian American and African American breast tumors by stage/menopause status.

<p>Intra-racial comparison of resistin gene expression of Caucasian American and African American breast tumors by stage/menopause status.</p

Resistin gene expression within Caucasian American and African American breast tumors by stage/receptor status.

<p>Resistin gene expression within Caucasian American and African American breast tumors by stage/receptor status.</p

Resistin gene expression between Caucasian American and African American breast tumors by stage/receptor status.

<p>Resistin gene expression between Caucasian American and African American breast tumors by stage/receptor status.</p

P-value of resistin gene expression between matched malignant and non-malignant breast samples.

<p>P-value of resistin gene expression between matched malignant and non-malignant breast samples.</p