Sample A: Cover Page of Thesis, Project, or Dissertation Proposal

ejecting the null hypothesis [8], and applied to the two datasets as interpreted by the BaFL
pipeline. This correction enabled us to elucidate a small subset of undeniably differentially
expressed genes as pertinent to lung cancer. The candidate list of genes when based on BaFL
pipeline values yields reasonable classification performance across 3 independent algorithms
when an appropriately sized dataset is used (Figure 4.8). The size of the data set is important:
when the Stearman dataset was used for training purposes all three models struggled, with the
BaFL data performing the best in all cases Statnikov, et al. used the Bhattacharjee multiclass data
in their pipeline for the cancer diagnosis and biomarker discovery, in which whey reported the
maximum prior probability of a dominant diagnostic category of 68.5% [24]. Their analysis
used the data in a training approach for 10 fold leave one out cross validation and reported perfect
prediction for the training model [24]. Additional analysis utilizing the full Bhattacharjee
multiclass dataset yielded binary classification accuracies of 52-56% for random forest and
support vector machines with and without gene down selection. While multiclass classificaiton,
with and without gene down selection yielded 77-82% for random forest and 89% for support
vector machines [25].
The relevance of these 31 genes is supported by the GO connections identified by the pathway
and literature search, PaLS, software (http://pals.bioinfo.cnio.es/), which connect 23 of the 30
genes (one ProbeSet aligns to no defined gene). KEGG pathway connections link 6 of these
genes, including opsteopontin, through focal adhesion and extra-cellular matrix receptor
intreraction [26]. Other extra cellular matrix genes include MFAP4, SPARCL1, ENG, RAMP3,
and LRRC32. SPARCL1 and SPOCK or SPARC like have been investigated for their role in
lung cancer [23]. These genes along with SPP1, MIF, and PECAM1 have strong immunological
associations and thereby may be essential for angiogenesis and tumorogenesis [19, 20, 27]. The
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