Step 2: In silico analysis

Goals

In this step our goal is to obtain information from the sequence of the selected gene to discover if its biological role can be related to neurodegeneration.

Given the sequence of the selected gene, you have to investigate if there are homologous genes in mouse (Mus musculus) and which biologic role play these genes in the mouse by analyzing their biochemical data and expression patterns. (If we found an homologous gene in Mus musculus, it is very probable that it develops similar functions in Mus musculus and humans, so giving us a clue about the function of the gene we are studying).

sequences

cDNA sequences

To do so, you will have to follow three steps:

    1. Find the most consistent translation of the cDNA
    2. Find the homologous genes that code for homologous proteins in Mus musculus.
    3. Stablish the expression pattern and function of the homologous gene in Mus musculus.

You will use bioinformatics research tools for In silico genetic investigations. Follow the steps as described in "How to proceed", and copy all your results and conclusions in the "Bioinformatic Lab Notebook" file. (LINK!)

At the end of this step, you will be able to justify if the gene you have chosen is likely to participate in neurodegenerative processes.

How to proceed

You will follow serveral steps, and at each step you have to sort your conclusions in a " "Bioinformatic Lab Notebook".

1) Find the most consistent translation of the cDNA.

    1. Open the Expasy bioinformatic tool to automatically translate the cDNA from the chosen gene in all the possible frames.
    2. Select the most consistent translation.
    3. Save your results and sort your conclusions in your Bioinformatic Lab Notebook..

2) Find homologous genes in Mouse and get informations about its biological function in mouse.

    1. Open the NCBI Blast Search Tool to look for other similar proteins in mouse (Mus musculus). BLAST-P will look in the www databases for proteins similar to the proteins you paste in the search box.
    2. After pasting the protein sequence in the search box, and pressing the BLAST button, let it search for some seconds.
    3. Select the highest score Mus musculus sequence (putative homologous of your gene in mouse) write its name. Discard the homologous genes from other species. When selected, look for informations about its biological role by clicking in the Gene section of the Related information menu at the right.
    4. Look at the informations (specially the GeneRIF section) to find clues about the function of this homologue of the gene you are studying. Some clues to interprete the function:
      1. Words indicating organs, tissues or cell types: astrocyte, renal, epidermic, osteoclast, retina, ...
      2. Words indicating protein categories: hormone, receptor, ligand, ...
      3. Words indicating actions: supressing, activating, growing, degenerating, protecting, transporting,...
    5. Confirm your results at UniProt Blast search. Look also for the 3D structure of its protein.
    6. Save your results in your "Bioinformatic Lab Notebook".

3) Stablish the suitability of the expression patterns of the Mus musculus homologous with a neurodegenerative-related function Use the informations below to analyze the expression patterns.

    1. Open the EMAGE Mouse atlas for the expression pattern of mouse genes.
    2. Write the name of the Mus musculus homologous of your gene and press "Go" to begin the search.
    3. Collect the data and expression patterns (both text and images).
    4. Save your results in your "Bioinformatic Lab Notebook".

4) Conclusion of this step: With all these data from the momologous gene in Mus musculus, you should be able to decide if the human gene you have chosen to study can still be a good candidate to develop a role in neurodegeneration in humans. Write it up in your "Bioinformatic Lab Notebook".

Key ideas to take into account

    • Genes contain some parts that are translated to protein (Exons), and some parts that are not (Introns).
    • When translated to protein, each combination of three ADN nucleotides (A,T,C,G) constitutes a codon, which codify for an amino acid, that can be represented by three (Cys, Lys, His,...) or one letter (C, K, H,..).
    • To work in molecular biology experiments, when extracted, mRNA is artificially retro-transcribed to cDNA, which is a version of the gene coding sequence without introns.
    • There are several reading frames for a given DNA sequence.
    • Some genes are conserved between species through evolution. When they conserve both its structure (sequence patterns) and function, we call it homologous genes.
    • Studying homologous genes in other animals can bring us information about these genes in humans.
    • Gene function is coherent with its expression pattern. Genes with an expression pattern associated to neurologic tissues -brain, nerves- are more likely to play a specific role in neurodegeneration.

BioInformatic Lab NoteBook

BioinformaticLabNoteBook