Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical Clustering

Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological relevance of the clusters that are subjected to subsequent scrutiny. The structure of the GO is another source of background knowledge that can be exploited through the use of semantic similarity. Results: We propose here a novel algorithm that integrates semantic similarities (derived from the ontology structure) into the procedure of deriving clusters from the dendrogram constructed during expression-based hierarchical clustering. Our approach can handle the multiple annotations, from different levels of the GO hierarchy, which most genes have. Moreover, it treats annotated and unannotated genes in a uniform manner. Consequently, the clusters obtained by our algorithm are characterized by significantly enriched annotations. In both cross-validation tests and when using an external index such as protein–protein interactions, our algorithm performs better than previous approaches. When applied to human cancer expression data, our algorithm identifies, among others, clusters of genes related to immune response and glucose metabolism. These clusters are also supported by protein–protein interaction data. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.Lynne and William Frankel Center for Computer Science; Paul Ivanier center for robotics research and production; National Institutes of Health (R01 HG003367-01A1

Deformations of the Boson sp(4,R)sp(4,R) Representation and its Subalgebras

The boson representation of the sp(4,R) algebra and two distinct deformations of it, are considered, as well as the compact and noncompact subalgebras of each. The initial as well as the deformed representations act in the same Fock space. One of the deformed representation is based on the standard q-deformation of the boson creation and annihilation operators. The subalgebras of sp(4,R) (compact u(2) and three representations of the noncompact u(1,1) are also deformed and are contained in this deformed algebra. They are reducible in the action spaces of sp(4,R) and decompose into irreducible representations. The other deformed representation, is realized by means of a transformation of the q-deformed bosons into q-tensors (spinor-like) with respect to the standard deformed su(2). All of its generators are deformed and have expressions in terms of tensor products of spinor-like operators. In this case, an other deformation of su(2) appears in a natural way as a subalgebra and can be interpreted as a deformation of the angular momentum algebra so(3). Its representation is reducible and decomposes into irreducible ones that yields a complete description of the same

Rate constants for the reactions of O+ with N2 and O2 as a function of temperature (300–1800 K)

This is the publisher's version, also available electronically from http://scitation.aip.org/content/aip/journal/jcp/106/9/10.1063/1.473450.We have studied the rate constants for the reaction of O+ with N2 over the temperature range 300–1600 K and the reaction of O+ with O2 over the range 300 to 1800 K. The results are in good agreement with previous measurements made up to 900 K. The rate constant for the O+reaction with N2 shows a minimum in the temperature range 1100–1300 K. The increase above this temperature is due to N2 v=2 becoming populated. The rate constant for O++O2 shows a minimum in the 800–1100 K range. Comparing to previous drift tube measurements allows the rate constant for O2 (v>0) to be derived. The v>0 rate constant is approximately five times larger than the v=0 rate constant

The Magnetic Electron Ion Spectrometer (MagEIS) Instruments Aboard the Radiation Belt Storm Probes (RBSP) Spacecraft

This paper describes the Magnetic Electron Ion Spectrometer (MagEIS) instruments aboard the RBSP spacecraft from an instrumentation and engineering point of view. There are four magnetic spectrometers aboard each of the two spacecraft, one low-energy unit (20–240 keV), two medium-energy units (80–1200 keV), and a high-energy unit (800–4800 keV). The high unit also contains a proton telescope (55 keV–20 MeV). The magnetic spectrometers focus electrons within a selected energy pass band upon a focal plane of several silicon detectors where pulse-height analysis is used to determine if the energy of the incident electron is appropriate for the electron momentum selected by the magnet. Thus each event is a two-parameter analysis, an approach leading to a greatly reduced background. The physics of these instruments are described in detail followed by the engineering implementation. The data outputs are described, and examples of the calibration results and early flight data presented

Magnetic states at the surface of alpha Fe2O3 thin films doped with Ti, Zn, or Sn

The spin states at the surface of epitaxial thin films of hematite, both undoped and doped with 1% Ti, Sn or Zn, respectively, were probed with x-ray magnetic linear dichroism (XMLD) spectroscopy. Morin transitions were observed for the undoped (T_M~200 K) and Sn-doped (T_M~300 K) cases, while Zn and Ti-doped samples were always in the high and low temperature phases, respectively. In contrast to what has been reported for bulk hematite doped with the tetravalent ions Sn4+ and Ti4+, for which T_M dramatically decreases, these dopants substantially increase T_M in thin films, far exceeding the bulk values. The normalized Fe LII-edge dichroism for T<T_M does not strongly depend on doping or temperature, except for an apparent increase of the peak amplitudes for T<100 K. We observed magnetic field-induced inversions of the dichroism peaks. By applying a magnetic field of 6.5 T on the Ti-doped sample, a transition into the T>T_M state was achieved. The temperature dependence of the critical field for the Sn-doped sample was characterized in detail. It was demonstrated the sample-to-sample variations of the Fe LIII-edge spectra were, for the most part, determined solely by the spin orientation state. Calculations of the polarization-depedent spectra based on a spin-multiplet model were in reasonable agreement with the experiment and showed a mixed excitation character of the peak structures.Comment: 8 pages, 8 figure

Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering

Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological relevance of the clusters that are subjected to subsequent scrutiny. The structure of the GO is another source of background knowledge that can be exploited through the use of semantic similarity