Theoretical Framework

Melanoma brain metastasis

This section includes the differential gene expression results of the three selected brain metastatic melanoma studies:

  • MBM-1:

    • Results obtained from the publication Molecular Profiling Reveals Unique Immune and Metabolic Features of Melanoma Brain Metastases. Link to the research article here
    • Comparision assessed: brain melanoma metastatic cells vs extracranial melanoma metastatic cells.

  • MBM-2:

    • Results obtained from the publication Dissecting the treatment-naive ecosystem of human melanoma brain metastasis. Link to the research article here
    • Comparison assessed: brain melanoma metastatic cells vs extracranial melanoma metastatic cells.

  • MBM-3:

    • Results obtained from the publication Decoding molecular programs in melanoma brain metastases. Link to the research article here
    • Comparison assessed: brain melanoma metastatic cells vs non tumor-bearing brain controls.

Neurodegenerative diseases

This section includes differential gene expression results and meta-analyses for Alzheimer’s disease (cortex and hippocampus regions), Parkinson’s disease (substantia nigra and striatum regions) and multiple sclerosis (brain region). For each neurodegenerative disease you will find:

  • Systematic review: multistep diagram with the flow of studies that have been discarded based on different exclusion criteria, as well as a summary table with the characteristics of the selected studies.

  • Individual analysis of selected studies, which incorporates the exploratory analyses -boxplots, principal component analysis (PCA) and clustering- to evaluate the sample distribution patterns, as well as the differential gene expression results considering the neurodegenerative disease and region.

    • Comparison assessed: cases vs controls.

  • Meta-analyses results, obtained by combining the differential gene expression results from each of the selected studies. Thus, it increases the statistical power and robustness compared to individual differential expression analyses. A meta-analysis by neurodegenerative disease and region has been performed:

    • AD-CT: meta-analyses for Alzheimer’s disease cortex region.
    • AD-HP: meta-analyses for Alzheimer’s disease hippocampus region.
    • PD-SN: meta-analyses for Parkinson’s disease substantia nigra region.
    • PD-ST: meta-analyses for Parkinson’s disease striatum region.
    • MS: meta-analyses for multiple sclerosis brain region.

Melanoma brain-specific metastasis signature

In this section the gene expression profile of brain melanoma metastatic cells versus extracranial melanoma metastatic cells is compared with the expression profile of neurodegenerative diseases. It is subdivided in:

  • Neurodegenerative signature: includes the panel of genes dysregulated in MBM-1, MBM-2 and at least one neurodegenerative disease (AD-CT, AD-HP, PD-SN, PD-ST and/or MS). Below you will find an interactive table with the genes dysregulated in MBM-1 and MBM-2. There you can check if they are also dysregulated in the neurodegenerative diseases, and what pattern they show.

  • Functional profiling: protein-protein interaction networks and overrepresented biological functions in the neurodegenerative signature. Results are divided by expression pattern and by neurodegenerative disease.

Melanoma brain metastasis tumoral signature

In this section the gene expression profile of brain melanoma metastatic cells versus non tumor-bearing brain controls is compared with the expression profile of neurodegenerative diseases. It is subdivided in:

  • Neurodegenerative signature: includes the panel of genes dysregulated in MBM-3 and at least one neurodegenerative disease (AD-CT, AD-HP, PD-SN, PD-ST and/or MS). Below you will find an interactive table with the genes dysregulated in MBM-3. There you can check if they are also dysregulated in the neurodegenerative diseases, and what pattern they show.

  • Functional profiling: protein-protein interaction networks and overrepresented biological functions in the neurodegenerative signature. Results are divided by expression pattern and by neurodegenerative disease.

Methods

Detailed description of the materials and methods applied to generate the results shown.

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