Resources

Lab protocols
Mouse models
Useful links

Useful links

Scientific & profesional networks

Scientific literature

Genomics and proteomics

Genome Databases and Tools

ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.

Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.

ENCODE: Encyclopedia of DNA Elements

GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~150 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information

Decipher – Mapping the Clinical Genome. DECIPHER is used by the clinical community to share and compare phenotypic and genotypic data. The DECIPHER database contains data from 28879 patients who have given consent for broad data-sharing

Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org)

Gene Expression

The Genotype-Tissue Expression (GTEx) project is an ongoing effort to build a comprehensive public resource to study tissue-specific gene expression and regulation. Samples were collected from 53 non-diseased tissue sites across nearly 1000 individuals, primarily for molecular assays including WGS, WES, and RNA-Seq. The GTEx Portal provides open access to data including gene expression, QTLs, and histology images.

MeV (Multiple Experiment Viewer) is a cloud-based application supporting analysis, visualization, and stratification of large genomic data, particularly for RNASeq and microarray data

Heatmapper is a freely available web server that allows users to interactively visualize their data in the form of heat maps through an easy-to-use graphical interface

Babelomics 5. Gene expression, genome variation and functional profiling analysis Suite

Enrichr: Comprehensive analysis of enrichment in a list of genes. Very useful! Published in
Chen et al. BMC Bioinformatics 2013 and Kuleshov et al. Nucleic Acids Research 2016.

Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes)

The Database for Annotation, Visualization and Integrated Discovery (DAVID ) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes

Gene Ontology Resource. The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. Ontology, annotations and other tools.

KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies

Cancer Genomics

The Oncomine™ Platform provides peer-reviewed analysis methods and a powerful set of analysis functions that compute gene expression signatures, clusters and gene-set modules, automatically extracting biological insights from cancer data

The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets

International Cancer Genome Consortium and Pancancer Analysis of Whole Genomes (PCAWG). Cancer genomics data sets visualization, analysis and download

COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world’s largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer

OASIS is an open-access web portal that enables cancer researchers to perform exploratory and integrative analyses of somatic mutation, copy number changes (CNV) and gene expression data from thousands of tumor, normal tissues and cell lines representing a broad spectrum of malignancies. By Pfizer

Oncoscape – Cancer Explorer

Kaplan-Meier Plotter, mRNA, RNAseq and microRNAs in breast, ovarian, lung, liver.. cancers

CellMiner – NCI-60 Analysis Tools

Protein analysis

The Human Protein Atlas aims to map all the human proteins in cells, tissues and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics and systems biology

PaxDB is a comprehensive absolute protein abundance database, which contains whole genome protein abundance information across organisms and tissues. PaxDb also provides the integrated datasets with higher coverage and better quality for each organism and tissue

NeXtprot. Exploring the universe of human proteins

PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor

Phosida allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest. It lists posttranslational modification sites associated with particular projects and proteomes or, alternatively, displays posttranslational modifications found for any protein or protein group of interest

PhosphoSitePlus provides comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, acetylation, and more.

STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases .

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System was designed to classify proteins (and their genes) in order to facilitate high-throughput analysis

PyMOL is a molecular visualization system. Visit PyMOL Wiki here.

Phyre2. Protein Homology/analogY Recognition Engine V 2.0. 3D simulation

Lab protocols & Techniques

Protocols.io. Open access repository for science methods

CRISPR Techniques

CRISPR Plasmids and Resources at Addgene

CrispRGold is a sgRNA design tool that searches for optimal sgRNA candidates in given genes or sequences. In addition to the specificity, CrispRGold filters for parameters important for the efficiency. (Graf R, Li X, Chu VT and Rajewsky K. 2019, Cell Reports 2019; Jan 29)

PCR Techniques

Primer3Plus. Select primers from a DNA sequence

The Gene Quantification platform describes and summarises all technical aspects involved in quantitative gene expression analysis using real-time qPCR & dPCR.  It presents a lot of new and innovative qPCR & dPCR applications, chemistries, methods, algorithms, MIQE and QC strategies, cyclers, kits, dyes, analysis methods, events, and services involved

Use the NEB Tm Calculator to estimate an appropriate annealing temperature when using NEB PCR products

Mouse Models

MGI is the international database resource at Jackson Laboratories for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.

Mouse Phenome Database. An integrated resource at Jackson Laboratories to explore physiology and behavior through genetics and genomics

International Mouse Strain Resource. The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains

International Mouse Phenotyping Consortium. The IMPC produces knockout mice and carry out high-throughput phenotyping of each line in order to determine the function of every gene in the mouse genome. These mice are preserved in repositories and made available to the scientific community. From 2011/12 onwards the IMPC will generate knockout mice and phenotype the remainder of the 20,000+ genes in a worldwide coordinated programme.

The KOMP Repository holds mouse models generated during the original Knockout Mouse Project (KOMP)

Software & Statistics

QuickCals – GraphPad software online

bioRender – Create Professional Science Figures

Related Networks and Labs

Networks

The MitoSys (systems biology of mitosis) project (EU-FP7 2010-2015) tackles mitosis from a systems biology perspective

The iLUNG Consortium on Lung Cancer at the Comunidad de Madrid

Related Research Labs

Angelika Amon’ lab at MIT, Cambridge

Andrew Burguess’ lab in Australia

Manuel Collado’s lab, Instituto de Investigación Sanitaria de Santiago, IDIS, dentro del Complejo Hospitalario Universitario de Santiago, CHUS, Santiago de Compostela

Fred Dick’s lab at Cancer Research Labs, Ontario

Silke Hauf’s lab At Virginia Tech (USA)

Tony Hyman’s lab at Max Planck Institute of Molecular Cell Biology & Genetics (Dresden, Germany)

Ignacio Pérez de Castro’s lab at ISCIII, Madrid

Stefano Santaguida’s lab at the European Institute of Oncology in Milano.

Piotr Sicinski’s lab at Dana Farber in Boston. See Piotr here expaning the research focus of his lab.

Jan M. Skotheim’s lab in Stanford (CA)

Stephen Taylor’s lab, Manchester Cancer Research Centre, UK