Revised eutherian gene collections.

OBJECTIVES: The most recent research projects in scientific field of eutherian comparative genomics included intentions to sequence every extant eutherian species genome in foreseeable future, so that future revisions and updates of eutherian gene data sets were expected. DATA DESCRIPTION: Using 35 public eutherian reference genomic sequence assemblies and free available software, the eutherian comparative genomic analysis protocol RRID:SCR_014401 was published as guidance against potential genomic sequence errors. The protocol curated 14 eutherian third-party data gene data sets, including, in aggregate, 2615 complete coding sequences that were deposited in European Nucleotide Archive. The published eutherian gene collections were used in revisions and updates of eutherian gene data set classifications and nomenclatures that included gene annotations, phylogenetic analyses and protein molecular evolution analyses.

Towards a multigene phylogeny of the Cymatosiraceae (Bacillariophyta, Mediophyceae) I: novel taxa within the subfamily cymatosiroideae based on molecular and morphological data.

The family Cymatosiraceae, composed of two subfamilies (Cymatosiroideae and Extubocelluloideae), are elongate, non-pennate diatoms and are commonly reported in marine planktonic and benthic assemblages all over the world. The combination of the gross bilateral symmetry of the frustule and radial symmetry of the valve poration, distinct pore fields at the valve apices and DNA sequence data place this family in the controversial diatom class Mediophyceae, sister to the pennate diatoms. The relationships of the Cymatosiraceae within the Mediophyceae, and the monophyly of the two cymatosiroid subfamilies, have become less stable with the addition of new DNA sequence data. In this paper, we examined 24 cymatosiraceaen strains, including the new taxa Lambertocellus africana (Dabek & Witkowski) Dabek, Witkowski & Ashworth comb. nov., Leyanella probus Ashworth, Dabek & Witkowski sp. nov., and Leyanella pauciporis Ashworth, Dabek & Park sp. nov. to create the most complete molecular phylogeny of the Cymatosiraceae to date, using a three-gene (SSU, rbcL and psbC) data set. The results of the phylogenetic analysis supported the monophyly of the Cymatosiraceae, but not the monophyly of the subfamilies Cymatosiroideae and Extubocelluloideae. The phylogenetic analysis also suggested a close relationship of the Cymatosiraceae to the family Eupodiscaceae. The phylogenetic results have lead us to re-evaluate the taxonomy of L. africana, which is sister to Cymatosira lorenziana rather than Minutocellus as suggested in the original description.

Cancer Bioinformatic Methods to Infer Meaningful Data From Small-Size Cohorts.

Whole-genome analyses have uncovered that most cancer-relevant genes cluster into 12 signaling pathways. Knowledge of the signaling pathways and associated gene signatures not only allows us to understand the mechanisms of oncogenesis inherent to specific cancers but also provides us with drug targets, molecular diagnostic and prognosis factors, as well as biomarkers for patient risk stratification and treatment. Publicly available genomic data sets constitute a wealth of gene mining opportunities for hypothesis generation and testing. However, the increasingly recognized genetic and epigenetic inter- and intratumor heterogeneity, combined with the preponderance of small-size cohorts, hamper reliable analysis and discovery. Here, we review two methods that are used to infer meaningful biological events from small-size data sets and discuss some of their applications and limitations.