https://bioinfo.cipf.es/WODA/ 2026-04-28T09:35:23+0200 https://bioinfo.cipf.es/WODA/ https://bioinfo.cipf.es/WODA/lib/tpl/prsnl10/images/favicon.ico text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/align_handson?rev=1547194864&do=diff Alignment: Practical session #!/bin/bash #move and create directory cd ~/mda12 mkdir -p mapping # index reference time bwa index resources/ref/human_g1k_v37.chr20.fasta time samtools faidx resources/ref/human_g1k_v37.chr20.fasta # align pair 1 time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\ resources/data/test_1.fq >\ mapping/test_1.sai # align pair 2 time bwa aln -t 1 -l 40 -k 2 resources/ref/human_g1k_v37.chr20.fasta\ resources/data/test_2.fq >\ mapping/test_… text/html 2022-11-23T12:11:00+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bbdd?rev=1669201860&do=diff A. Functional profiling for genes In several omic scenarios we have a group of genes of interest from a transcriptomic analysis, or from different genomic studies where we have found causal variants of a certain disease or even a selection of genes obtained after a literature review. text/html 2019-11-19T10:19:16+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bbdd_ej1?rev=1574155156&do=diff ¿Cómo obtener la anotación funcional desde BioMart? Nos dirigimos a la web de BioMart. * Escogemos la base de datos “Ensembl Genes”. * Elegimos el organismo con el que estemos trabajando. * Si quisiéramos restringir la búsqueda a un número de genes determinados (por ejemplo los que estén en un cromosoma específico), lo indicaríamos en text/html 2019-11-19T10:19:44+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bbdd_ej2?rev=1574155184&do=diff Anotación funcional para plantas desde Biomart Ensembl Nos dirigimos a la web de BioMart. * Escogemos la base de datos “Ensembl Plants”. * Elegimos el organismo con el que estemos trabajando: Arabidopsis Thaliana. * Si quisiéramos restringir la búsqueda a un número de genes determinados (por ejemplo los que estén en un cromosoma específico), lo indicaríamos en text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex1?rev=1547194864&do=diff Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex2?rev=1547194864&do=diff Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex3?rev=1547194864&do=diff Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex4?rev=1547194864&do=diff Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex5?rev=1547194864&do=diff Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex6?rev=1547194864&do=diff Exercise 6 Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex7?rev=1547194864&do=diff Exercise 7 Data description Working plan If we have a clear profile of mutation, we will have to apply these filters on BiERapp to get directly the possible causal mutation. Sometimes we have several interesting profiles of mutations, not only one. For this case we should explore these different scenarios and decide the best prioritization strategy. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex8?rev=1547194864&do=diff Exercise 8 Data description: cases vs. controls Working plan How many variants do you detect for each scenario? A. Individual filters * Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs? * Reference for all controls and homozygous variant for all cases. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex9?rev=1547194864&do=diff Exercise 9 Data description Working plan We have several candidate profiles of mutations to explore: How many variants do you detect for each scenario? A. Individual filters * Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs? * Recessive heritage text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_ex10?rev=1547194864&do=diff Exercise 10 Data description Working plan We have several candidate profiles of mutations to explore: How many variants do you detect for each scenario? A. Individual filters * Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs? * Recessive heritage text/html 2019-01-11T13:04:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/bierapp_exercises?rev=1547208244&do=diff Prioritization of variants and genes: BiERapp Check!!!!!<http://bioinfo.cipf.es/mbb/doku.php/bierapp_exercises> These exercises show how to analyze exome data for different families or groups. Goal is to detect associated mutations to Mendelian disease. Input data is a set of VCF files. Output analysis will be a selection of candidate variants. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_arabidopsis?rev=1547194864&do=diff Evaluación de la expresión génica en Arabidopsis bajo condiciones de alta luz Objetivo Detectar marcadores transcriptómicos que caractericen el impacto de condiciones de alta luz en Arabidopsis. Información detallada en la publicación: Early transcriptional defense responses in Arabidopsis cell suspension culture under high-light conditions. Plant Physiol 2011 Jul;156(3):1439-56. PMID: 21531897 text/html 2024-11-22T18:42:32+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_ex1?rev=1732297352&do=diff Activity 1 The analysis of gene expression will allow us to know the different levels of expression between various groups of interest, for example between sick and healthy people. This information is very interesting because it helps us to better understand the molecular mechanisms of a disease, it will facilitate the detection of biomarkers, text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_ex2?rev=1547194864&do=diff Actividad 2. Determinación de biomarcadores en un estudio metabolómico Objetivo Detectar marcadores metabolómicos en pacientes con cáncer de pulmón. Datos Disponemos de 2 grupos de sujetos: 5 pacientes con cáncer de pulmón (LC) y 5 pacientes sanos (CONTROL) en los que se han evaluado el nivel de 22 metabolitos de interés. text/html 2019-03-06T18:46:48+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_ex3?rev=1551894408&do=diff Aplicaciones NGS en estudios transcriptómicos Esta práctica incluye varios ejercicios para trabajar con los diferentes módulos de análisis que nos ofrece la suite Babelomics 5. Desde el navegador Firefox iremos al siguiente enlace: <http://babelomics.bioinfo.cipf.es/> * Preprocessing for RNA-Seq and microRNA-Seq text/html 2019-03-06T18:50:25+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_rnaseq1?rev=1551894625&do=diff Actividad 4.1. Análisis de datos de RNA-Seq: diferencia de expresión entre grupos Objetivo Queremos conocer mejor los mecanismos moleculares de una determinada enfermedad compleja en la que sabemos que una determinada hormona tiene un papel importante. Para ellos diseñamos un experimento caso-control utilizando RNA-Seq en ratón, donde estamos interesamos en detectar genes diferencialmente expresados entre estos 2 grupos: wild type (WT) y tratados con hormona T3 . text/html 2019-03-06T18:50:38+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_rnaseq2?rev=1551894638&do=diff Actividad 4.2. Detección de patrones de expresión entre pacientes con tumores de riñón y pulmón Objetivo Detectar genes diferencialmente expresados entre 2 grupos de inviduos en un estudio de cáncer. Datos Disponemos de conteos no normalizados en 29.405 genes para un total de 10 individuos. Estos datos se obtuvieron tras aplicar un análisis primario que incluyó la evaluación de calidad de las secuencias, mapeo y cuantificación de la expresión a nivel de gen. text/html 2019-03-06T18:50:50+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_rnaseq3?rev=1551894650&do=diff Actividad 4.3. Análisis de datos de microRNA-Seq: Diferencia de expresión entre grupos experimentales Objetivo Detectar biomarcadores de cáncer de pulmón en estudios de miRNAS. Datos * Disponemos de conteos normalizados en 849 microRNAs para un total de 30 individuos: 23 enfermos de cáncer de pulmón y 7 sanos. text/html 2019-01-11T13:11:55+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/biomarkers_rnaseq4?rev=1547208715&do=diff Practical exercises * Normalization exercise * Differential expression exercise * Single Enrichment exercise * Clustering exercise text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/calling_handson?rev=1547194864&do=diff Variant calling and annotation: Practical session #!/bin/bash # Working directory cd ~/mda12/calling # Run program and see options ~/mda12/calling/software/GenomeAnalysisTK-1.4-15-gcd43f01/GenomeAnalysisTK.jar # UnifiedGenotyper ~/mda12/calling/software/GenomeAnalysisTK-1.4-15-gcd43f01/GenomeAnalysisTK.jar\ -T UnifiedGenotyper # Checking the reference head ~/mda12/resources/ref/human_g1k_v37.chr20.fasta head -3000 ~/mda12/resources/ref/human_g1k_v37.chr20.fasta | tail #Checking t… text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/cipf?rev=1547194864&do=diff The Centro de Investigacion Principe Felipe is a research center focused on regenerative medicine and drug discovery. Visit our web page at: <http://www.cipf.es> [Centro de Investigacion Principe Felipe] text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/contact?rev=1547194864&do=diff Contact <ubb@cipf.es>. Unidad de Bionformática y Bioestadística. Centro de Investigación Príncipe Felipe. Tel: 96 328 96 80, ext.: 2003 Address: C/ Eduardo Primo Yúfera, 3 (Junto al Oceanografico) 46012 Valencia, Spain. See map ---------- <http://bioinfo.cipf.es/ubb> <http://www.cipf.es> text/html 2019-01-11T13:01:57+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/csvs_exercises?rev=1547208117&do=diff CIBERER Spanish Variant Server Estos ejercicios nos muestran cómo obtener información sobre la variabilidad de la población española en diversos escenarios de interés. La herramienta es útil para filtrar polimorfismos y variaciones locales, en el proceso de priorización de genes candidatos para determinadas enfermedades. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/deadlines_and_important_dates?rev=1547194864&do=diff Deadlines and important dates: * Course: Wed, 11/07/2012 (All day) - Thu, 12/07/2012 (All day) text/html 2019-03-07T13:08:50+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/downloads?rev=1551960530&do=diff Downloads * 2019, Máster en Bioinformática Aplicada a Medicina Personalizada y Salud. Madrid. [Presentaciones] * Alberto: text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/equipment?rev=1547194864&do=diff Course Equipment text/html 2024-11-22T17:23:06+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ex_biomarkers?rev=1732292586&do=diff OMICS-BASED BIOMARKERS DETECTION * Activity 1. Detection of therapeutic targets using a gene expression study with microarrays * Activity 2. Biomarker determination in a metabolomics study * Activity 3. Assessment of gene expression in Arabidopsis under high light conditions * Activity 4. Biomarker studies with RNA-Seq data * More activities text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ex_ppi?rev=1547194864&do=diff Redes de interacción proteína-proteína Introducción En múltiples investigaciones generamos diferentes de datos ómicos: * un grupo de genes o proteínas de interés procedentes de un estudio transcriptómico o proteómico * un grupo de genes detectados en diversos estudios genómicos, donde hemos encontrado variantes causales de una determinada enfermedad text/html 2019-11-19T11:43:54+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_1?rev=1574160234&do=diff Evaluación funcional del efecto de hormona T3 en estudio transcriptómico Objetivo Caracterizar funcionalmente mediante diferentes estrategias de enriquecimiento (métodos de sobrerrepresentación y GSEA), los resultados obtenidos en el análisis de la expresión diferencial del experimento donde utilizamos RNA-Seq en ratón, y en el que estábamos interesamos en detectar genes diferencialmente expresados entre estos 2 grupos: wild type (WT) y tratados con hormona T3. text/html 2021-03-06T09:20:43+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_2?rev=1615018843&do=diff Functional characterization of genes associated with retinal dystrophies There are several methods of functional enrichment. From the web tool PANTHER we will perform several approaches to know the functions in which our list of genes of interest are participating. text/html 2021-03-06T09:15:22+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_3?rev=1615018522&do=diff Functional evaluation of the effect of T3 hormone in a transcriptomic study * There are several methods of functional enrichment that can be used from various web tools and programming languages. * We will start using the web tool PANTHER where we will perform several approaches to know the functions in which our list of genes of interest are participating. text/html 2022-11-23T09:56:31+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_3b?rev=1669193791&do=diff Plan de trabajo Seguimos con el ejemplo “Evaluación funcional del efecto de hormona T3 en estudio transcriptómico con datos de RNA-Seq”. En este caso realizaremos una caracterización funcional con un método GSA utilizando R. En esta [carpeta comprimida:] encontrarás text/html 2022-11-23T09:59:03+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_3c?rev=1669193943&do=diff Plan de trabajo * Descarga y descomprime la [carpeta]. * Ejecuta el script de R para familiarizarte con los métodos de caracterización funcional desde el paquete clusterProfiler. * Este manual detallado te orientará sobre algunos aspectos de estos procedimientos. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_4?rev=1547194864&do=diff Plan de trabajo En un estudio transcriptómico con datos de RNA-Seq disponíamos de dos grupos experimentales: casos y controles. Tras realizar el análisis de expresión diferencial obtuvimos los siguientes resultados que te puedes descargar en este text/html 2021-03-06T11:20:54+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_5?rev=1615026054&do=diff Functional characterization of transcriptomic differences between lung cancer and kidney cancer * There are several methods of functional enrichment that can be used from various web tools and programming languages. * We will start by using the web tool text/html 2019-03-06T18:55:47+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_micro1?rev=1551894947&do=diff Functional profiling in microRNAs study about lung cancer Goal Functional characterization for microRNAs biomarkers in lung cancer study. Data * We have normalized counts in 849 microRNAs for a total of 30 individuals: 23 lung cancer patients and 7 healthy ones. text/html 2019-11-30T21:47:15+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_r1?rev=1575146835&do=diff text/html 2019-11-19T15:27:17+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/fp_r2?rev=1574173637&do=diff clusterProfiler package implements methods to analyze and visualize functional profiles GO, KEGG, DisGeNET, Reactome...) of gene and gene clusters. Could you repeat previous exercises using clusterProfiler package? Here you have script + data to practice: More detailed information text/html 2019-02-14T19:01:34+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/geo_gene_expression_omnibus?rev=1550167294&do=diff Gene Expression Omnibus GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/going_out_in_valencia?rev=1547194864&do=diff Going out in Valencia There are several areas in Valencia with a lot of activity: music, dancing, bars.... To start to know our city, we recommend you: historial center, Russafa or Benimaclet but there are other trendy places! * Every Wednesday there is an interesting auction in text/html 2019-06-26T11:09:54+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/home?rev=1561540194&do=diff ---------- ---------- What is WODA? WODA (Web-based Omics Data Analysis) is a practical course to learn how to perform omics data analysis from webtools. What is this course for? Questions such as How can I find the causative mutation of the disease in this family? or What pathways are activated in my RNA-seq experiment? are becoming more frequent as text/html 2019-02-17T18:53:15+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/imageo?rev=1550425995&do=diff ImaGEO: Integrative Gene Expression Meta-Analysis from GEO database Summary. The Gene Expression Omnibus (GEO) database provides an invaluable resource of publicly available gene expression data that can be integrated and analyzed to derive new hypothesis and knowledge. In this context, gene expression meta-analysis (geMAs) is increasingly used in several fields to improve study reproducibility and discovering robust biomarkers. Nevertheless, integrating data is not straightforward without bi… text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/map?rev=1547194864&do=diff How to arrive See the map to find the CIPF location. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/menu?rev=1547194864&do=diff Menú Primero + segundo + postre/café + bebida MIÉRCOLES 24 DE OCTUBRE DE 2018 * Ensalada de temporada * Garbanzos y espinacas * Jamoncitos de pollo a la cazadora * Merluza al horno * Fruta de temporada, natillas caseras y tartas JUEVES 25 DE OCTUBRE DE 2018 text/html 2019-02-17T18:55:17+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/networkanalyst?rev=1550426117&do=diff NetworkAnalyst A visual analytics platform for comprehensive gene expression profiling & meta-analysis * NetworkAnalyst text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ngstutorial?rev=1547194864&do=diff Quality Control Preliminaries Software used in this practical: * FastQC: A quality control tool for high-throughput sequencing data. * cutadapt: A tool to remove adapter sequences from high-throughput sequencing data. File formats explored in this practical text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ppi0?rev=1547194864&do=diff Comenzando a trabajar con STRING * Esta herramienta web es muy útil para conocer las relaciones de conexión proteína-proteína de una o varias proteínas. * Es posible proporcionar diversos identificadores de gen o proteína y de forma automatizada se realizará la evaluación funcional a nivel de proteína. text/html 2025-05-19T17:35:39+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ppi1?rev=1747668939&do=diff Caracterización funcional de proteínas asociadas a envecimiento Tras realizar un estudio de proteómica sobre envejecimiento en humano, hemos detectado un grupo de 11 proteínas con intensidad diferencial significativa entre varios grupos experimentales. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ppi2?rev=1547194864&do=diff Genes candidatos en retinitis La secuenciación de exomas es útil en el descubrimiento de nuevas variantes de interés. Tras valorar un determinado número de sujetos, es posible detectar la presencia repetida de algunas de estas variantes en determinadas enfermedades. Estos genes serían unos buenos candidatos en el diseño de un panel de genes orientado al diagnóstico de estas patologías. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ppi3?rev=1547194864&do=diff Evaluación del efecto de hormona T3 en estudio transcriptómico Objetivo Caracterizar funcionalmente mediante una análisis de interacción proteína-proteína, los resultados obtenidos en el análisis de la expresión diferencial del experimento donde utilizamos RNA-Seq en ratón, y en el que estábamos interesamos en detectar genes diferencialmente expresados entre estos 2 grupos: wild type (WT) y tratados con hormona T3. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/ppi4?rev=1547194864&do=diff Caracterización funcional mediante redes de interacción proteína-proteína en estudio transcriptómico En un estudio transcriptómico con datos de RNA-Seq disponíamos de dos grupos experimentales: casos y controles. Tras realizar el análisis de expresión diferencial obtuvimos los siguientes resultados que te puedes descargar en este text/html 2022-02-20T10:01:45+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/program?rev=1645347705&do=diff A. Introduction * [Overview] * [Clinical and biological databases, Statistics and high throughput technologies] B. Omics-based biomarkers detection * [Omics-based biomarkers detection] * Tool: Babelomics (<http://babelomics.bioinfo.cipf.es/> from Firefox browser) * Exercises * Metabolomics, Proteomics, Transcriptomics from arrays,... * RNA-Seq, microRNA-Seq,... C. Classification C.1. Unsupervised classification text/html 2019-02-17T18:51:52+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/references?rev=1550425912&do=diff References and links * High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. Hidalgo MR, Cubuk C, Amadoz A, Salavert F, Carbonell-Caballero J, Dopazo J. Oncotarget. 2017;8(3):5160-5178 * Integrated gene set analysis for microRNA studies. text/html 2019-02-16T18:56:26+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/resources?rev=1550339786&do=diff * Máster Universitario en Bioinformática y Biología Computacional, UAM, Feb 2019. [Presentaciones]. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/sidebar?rev=1547194864&do=diff COURSE * Home * Program * Teachers * Bioinformatics at CIPF LOGISTICS * Contact * Deadlines and important dates * Map * Accomodation * More courses at CIPF text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/social_dinner?rev=1547194864&do=diff Social dinners 1. Genomics Module * When? Tuesday 7th March 2017 at 21:00. * Where? Delicat restaurant in carrer del Comte d'Almodóvar, 4, 46003 València. It is a cozy restaurant sited in the Ciutat Vella district, in the heart of the old town, near the Virgen's square and the Cathedral. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/software_list?rev=1547194864&do=diff Software list Clinical and biological databases: * Ensembl (<https://www.ensembl.org/index.html>) * Ciberer Spanish Variant Server (<http://csvs.babelomics.org/>) * Gene Expression Omnibus (<https://www.ncbi.nlm.nih.gov/geo/>) Visualization: * BoxPlotR (<http://boxplot.tyerslab.com>) * Heatmapper (<http://heatmapper.ca>) Omics-based biomarkers detection and functional profiling: * text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/teachers?rev=1547194864&do=diff Teachers * Antonio Jordán Pla, antonio.jordan@uv.es, Dept. Genómica Funcional de Levaduras. Universitat de València * Francisco García García, fgarcia@cipf.es, UBB-CIPF * José Francisco Català Senent, jfcatala@cipf.es, UBB-CIPF text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/team_design?rev=1547194864&do=diff Activity 2 Create new user and upload the data * Please create your own user and login with this new user. * Upload the required VCF file in “Default Study” and wait 4-5 min to indexing tool. <http://bioinfo.cipf.es/apps-beta/gda16/team/patients.vcf> * While the file is indexing we will design all the panels. text/html 2019-01-11T09:21:04+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/team_ex1?rev=1547194864&do=diff Activity 1 A. Working plan * Create a new gene panel including variants related Charcot-Marie-Tooth disease. * Upload data for 10 patients to evaluate possible candidate variants (VCF files): (this step is ready for you) * Create a new project + study: CMT. text/html 2019-01-11T13:04:47+0200 Anonymous (anonymous@undisclosed.example.com) https://bioinfo.cipf.es/WODA/doku.php/team_exercises?rev=1547208287&do=diff TEAM: Targeted Enrichment Analysis and Management IMPORTANT: CHECK <http://bioinfo.cipf.es/mbb/doku.php/team_exercises> These exercises show how to design and analyze panel genes in the clinical context oriented to diagnosis. * Input: one or several VCF files and a panel gene. * Output: different formats of results, including selected variants related to a specific disease.