eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks

While gene expression data at the mRNA level can be globally and accurately measured, profiling the activity of cell signaling pathways is currently much more difficult. eXpression2Kinases (X2K) computationally predicts involvement of upstream cell signaling pathways, given a signature of differentially expressed genes. X2K first computes enrichment for transcription factors likely to regulate the expression of the differentially expressed genes. The next step of X2K connects these enriched transcription factors through known protein–protein interactions (PPIs) to construct a subnetwork. The final step performs kinase enrichment analysis on the members of the subnetwork. X2K Web is a new implementation of the original eXpression2Kinases algorithm with important enhancements. X2K Web includes many new transcription factor and kinase libraries, and PPI networks. For demonstration, thousands of gene expression signatures induced by kinase inhibitors, applied to six breast cancer cell lines, are provided for fetching directly into X2K Web. The results are displayed as interactive downloadable vector graphic network images and bar graphs. Benchmarking various settings via random permutations enabled the identification of an optimal set of parameters to be used as the default settings in X2K Web. X2K Web is freely available from http://X2K.cloud

The SCUBA-2 Cosmology Legacy Survey: 850um maps, catalogues and number counts

We present a catalogue of ∼3,000 submillimetre sources detected (≥3.5σ) at 850μm over ∼5 deg2 surveyed as part of the James Clerk Maxwell Telescope (JCMT) SCUBA-2 Cosmology Legacy Survey (S2CLS). This is the largest survey of its kind at 850μm, increasing the sample size of 850-μm-selected submillimetre galaxies by an order of magnitude. The wide 850μm survey component of S2CLS covers the extragalactic fields: UKIDSS-UDS, COSMOS, Akari-NEP, Extended Groth Strip, Lockman Hole North, SSA22 and GOODS-North. The average 1σ depth of S2CLS is 1.2 mJy beam−1, approaching the SCUBA-2 850μm confusion limit, which we determine to be σc ≈ 0.8 mJy beam−1. We measure the 850μm number counts, reducing the Poisson errors on the differential counts to approximately 4% at S850 ≈ 3 mJy. With several independent fields, we investigate field-to-field variance, finding that the number counts on 0.5–1° scales are generally within 50% of the S2CLS mean for S850 > 3 mJy, with scatter consistent with the Poisson and estimated cosmic variance uncertainties, although there is a marginal (2σ) density enhancement in GOODS-North. The observed counts are in reasonable agreement with recent phenomenological and semi-analytic models, although determining the shape of the faint end slope (S850 < 3 mJy) remains a key test. The large solid angle of S2CLS allows us to measure the bright-end counts: at S850 > 10 mJy there are approximately ten sources per square degree, and we detect the distinctive up-turn in the number counts indicative of the detection of local sources of 850μm emission, and strongly lensed high-redshift galaxies. All calibrated maps and the catalogue are made publicly available