‘Gene shaving’ as a method for identifying distinct sets of genes with similar expression patterns

Background: Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called ‘gene shaving’. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other widely used methods for analyzing gene expression studies in that genes may belong to more than one cluster, and the clustering may be supervised by an outcome measure. The technique can be ‘unsupervised’, that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings. Results: We illustrate the use of the gene shaving method to analyze gene expression measurements made on samples from patients with diffuse large B-cell lymphoma. The method identifies a small cluster of genes whose expression is highly predictive of survival. Conclusions: The gene shaving method is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worth further investigation.

Acoustic Detections of Singing Humpback Whales in Deep Waters Off The British Isles

From October 1996 through September 1998, we used bottom-mounted hydrophone arrays to monitor deep-water areas north and west of the British Isles for songs of humpback whales (Megaptera novaeangliae). Singing humpbacks were consistently detected between October and March from the Shetland- Faroe Islands south to waters west of the English Channel. Temporal and geographic patterns of song detections, and movements of individually tracked whales, exhibited a southwesterly trend over this period, but with no corresponding northward trend between April and September. These results, together with a review of historical data from this area, suggest that the offshore waters of the British Isles represent a migration corridor for humpbacks, at least some of which summer in Norwegian (and possibly eastern Icelandic) waters. The migratory destination of the detected animals remains unknown, but the limited data suggest that these whales are bound primarily for the West Indies rather than historical breeding areas off the northwestern coast of Africa. Humpbacks detected in British waters after early to mid- March probably do not undertake a full migration to the tropics. These data provide further evidence that singing is not confined to tropical waters in winter, but occurs commonly on migration even in high latitudes.

Seasonal Variation in Reception of Fin Whale Calls at Five Geographic Areas in the North Pacific

In late August 1991 scientists at the National Oceanic and Atmospheric Administration’s (NOAA) National Marine Mammal Laboratory (NMML) and Pacific Marine Environmental Laboratory (PMEL) began a pilot study to investigate the capability of hydrophones from the US. Navy’s fixed array system to detect large whales in the North Pacific by passive reception of their calls. PMEL had previously established a direct data link from five bottom-mounted arrays of the Navy SOSUS (Sound Surveillance System), via the Naval Oceanographic Processing Facility (NOPF) at Whidbey Island, Washington, to study low-level seafloor seismicity (Fox et al. 1994). PMEL subsequently provided NMML tapes of SOSUS hydrophone data from which whale calls were analyzed. As in an analogous study conducted in the North Atlantic (Nishimura and Conlon 1994, Clark 1995, Mellinger and Clark 1995), calls attributable to whales were received at each SOSUS site at rates that varied seasonally (Anonymous 1996).