Additional file 2 of RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor

Additional file 2. Supplementary figure of the use case 1, showing the top 20 genes by number of mutations across the 217 patients under analysis, orderly and proportionally plotted horizontally by their gene length, from left (VHL - 12,036 bp) to right (PCDHA@ - 226,209 bp

Additional file 4 of RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor

Additional file 4. Supplementary figure of the use case 2, showing the optimal number of clusters based on the average silhouette widt

Additional file 1 of RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor

Additional file 1. Supplementary figure of the use case 1, showing the counts of mutated genes for each KIRC patient younger than 65 year

Additional file 3 of RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor

Additional file 3. Flowchart of the main steps of use case 2. As illustrated, starting from both local and remote gene expression datasets, a RGMQL mixed processing first joins the two datasets remotely, then downloads and processes the result locally. After the generation of a samples-per-genes dataset, also the main phases of local post-processing with clustering analysis are depicte

Additional file 5 of RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor

Additional file 5. Flowchart of the main steps of use case 3. As illustrated, after RGMQL remote pre-processing of the ENCODE ChIP-seq datasets of interest, two independent but related RGMQL processing are performed. The first one computes the threshold needed to select the DNA regions on which the transcription factor (TF) accumulation must be assessed. The second one uses the threshold to select such regions, and process them up to find HOT DNA zones by cooperating with the TFHAZ Bioconductor packag

MicroGen: a MIAME compliant web system for microarray experiment information and workflow management-1

<p><b>Copyright information:</b></p><p>Taken from "MicroGen: a MIAME compliant web system for microarray experiment information and workflow management"</p><p></p><p>BMC Bioinformatics 2005;6(Suppl 4):S6-S6.</p><p>Published online 1 Dec 2005</p><p>PMCID:PMC1866379.</p><p></p

Additional file 2 of Genomic data integration and user-defined sample-set extraction for population variant analysis

Additional file 2. Example of transformed metadata: In this .xlsx (MS Excel) file, we list all the output metadata categories generated for each sample from the transformation of the 1KGP input datasets. The output metadata include information collected from all the four 1KGP metadata files considered. Some categories are not reported in the source metadata files—they are identified by the label manually_curated__...—and were added by the developed pipeline to store technical details (e.g., download date, the md5 hash of the source file, file size, etc.) and information derived from the knowledge of the source, such as the species, the processing pipeline used in the source and the health status. For every information category, the table reports a possible value. The third column (cardinality > 1) tells whether the same key can appear multiple times in the output GDM metadata file. This is used to represent multi-valued metadata categories; for example, in a GDM metadata file, the key manually_curated__chromosome appears once for every chromosome mutated by the variants of the sample

Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists-0

<p><b>Copyright information:</b></p><p>Taken from "Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S14</p><p>BMC Bioinformatics 2007;8(Suppl 1):S14-S14.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885843.</p><p></p>ro entry (D: protein domain); Tree: tree label in the defined protein domain parent/child hierarchy, if any; Level: level in the related tree of the defined protein domain parent/child hierarchy, if any (higher levels correspond to more specific protein domains); Num. (%): absolute and percentage number of considered genes that codify proteins containing the specific protein domain (Category Name)

Additional file 1 of Identification of transcription factor high accumulation DNA zones

Additional file 1.  Supplementary Material

Los dobles participios en español: Estudio de corpus

Some verbs in Spanish present in their non-finite verb form of past participles the possibility of possessing both a regular and an irregular form: 'Freído'/'frito'(fried), 'imprimido'/'impreso' (printed), etc. It is well known that the past participle may function both as a verb and as an adjective, and this universality makes it particularly interesting to observe how these doublets of participles are applied and in which contexts they appear in contemporary Spanish, aspect this investigation wish to elaborate. In order to delimit the investigation and to be able to provide sufficiently detailed descriptions, we will focus the study on the four participles pairs, that is, 'bendecido'/'bendito' (from the verb 'bendecir' [to bless]), 'freído'/'frito' (from the verb 'freír' [to fry]), 'imprimido'/'impreso' (from the verbo 'imprimir' [to print]) and 'corrompido'/'corrupto' (from the verb 'corromper' [to corrupt]). We have through in-depth analysis of examples found in various corpus of the Spanish language (i.e. El corpus de CREA and El corpus del Español de Davies) discovered that they show distributional differences when it comes to this double functionality of the participles. It appears that the regular forms 'bendecido', 'freído' and 'imprimido' are exclusively verbal forms, while the irregular participles 'bendito' and 'corrupto' always receive adjectival interpretations. The regular form 'corrompido' and the irregular participles 'frito' and 'impreso', on the other hand, may alternate between the two possible functions. Furthermore, this thesis relates the discoveries with two fundamental morphological theories, that is, lexicalism and constructionism. None of these two linguistic theories as they are formulated today provide appropriate explanations, and therefore we suggest that it is necessary to address each verb separately in order to understand the alternation between the two participial forms, considering the syntactic, semantic and even geographic factors of each verb