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Motivation: Recent developments in experimental methods facilitate increasingly larger signal transduction datasets. Two main approaches can be taken to derive a mathematical model from these data: training a network (obtained, e.g., from literature) to the data, or inferring the network from the data alone. Purely data-driven methods scale up poorly and have limited interpretability, whereas literature-constrained methods cannot deal with incomplete networks.Results: We present an efficient approach, implemented in the R package CNORfeeder, to integrate literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. Our method extends a given network with links derived from the data via various inference methods, and uses information on physical interactions of proteins to guide and validate the integration of links. We apply CNORfeeder to a network of growth and inflammatory signalling. We obtain a model with superior data fit in the human liver cancer HepG2 and propose potential missing pathways.Availability: CNORfeeder is in the process of being submitted to Bioconductor and in the meantime available at www.cellnopt.org.Contact: saezrodriguez@ebi.ac.ukSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Background and Purpose: Transient receptor potential ankyrin 1 (TRPA1) channels are expressed by primary afferent neurones and activated by irritant chemicals including allyl isothiocyanate (AITC). Here we investigated whether intracolonic AITC causes afferent input to the spinal cord and whether this response is modified by mild colitis, morphine or a TRPA1 channel blocker.Experimental Approach: One hour after intracolonic administration of AITC to female mice, afferent signalling was visualized by expression of c-Fos in laminae I-II(o) of the spinal dorsal horn at sacral segment S1. Mild colitis was induced by dextran sulphate sodium (DSS) added to drinking water for 1 week.Key Results: Relative to vehicle, AITC (2%) increased expression of c-Fos in the spinal cord. Following induction of mild colitis by DSS (2%), spinal c-Fos responses to AITC, but not vehicle, were augmented by 41%. Colonic inflammation was present (increased myeloperoxidase content and disease activity score), whereas colonic histology, locomotion, feeding and drinking remained unchanged. Morphine (10 mg.kg(-1)) or the TRPA1 channel blocker HC-030031 (300 mg.kg(-1)) inhibited the spinal c-Fos response to AITC, in control and DSS-pretreated animals, whereas the response to intracolonic capsaicin (5%) was blocked by morphine but not HC-030031.Conclusions and Implications: Activation of colonic TRPA1 channels is signalled to the spinal cord. Mild colitis enhanced this afferent input that, as it is sensitive to morphine, is most likely of a chemonociceptive nature. As several irritant chemicals can be present in chyme, TRPA1 channels may mediate several gastrointestinal pain conditions. [ABSTRACT FROM AUTHOR]