Analysis of cell migration in gliomas

Several datasets are analyzed regarding an in vitro culture of cells from patients with gliomas.

Dataset description

The datasets provided for the study were processed and divided into 3 main datasets based on common characteristics to allow for better data analysis.

Enrichment Dataset:

Enrichment Dataset has 17 columns and the description of each one is reported here below:

• QUERY: ?

• SIGNIFICANT: ?

• P_VALUE: a probability value between 0 and 1. It helps to decide whether the differences observed in gene expression are likely due to chance or a real biological effect. A lower p-value suggests that it's unlikely the observed difference occurred by random chance.

• TERM_SIZE: ?

• QUERY_SIZE: ?

• INTERSECTION_SIZE: ?

• PRECISION: measures how many of the genes the algorithm predicted as relevant are actually relevant .

• RECALL: measures how many of the truly relevant genes the algorithm was able to find.

• TERM_ID: It is a unique seven-digit identifier (GO ID) that is assigned to each concept within the Gene Ontology (GO). This ID serves as the primary way to reference and retrieve specific information about that concept

• SOURCE: ?

• TERM_NAME: Gene ontology human-readable term name of the term_id that describe the concept

• EFFECTIVE_DOMAIN_SIZE: ?

• SOURCE_ORDER: ?

• PARENTS: An array containing the GO IDs of the parent terms within the Gene Ontology (GO) hierarchy. The term specified in term_id is a more specialized subtype of these parent concepts.

• REGULATION: indicates the type of regulation of gene expression, it can be "Downregulated" or "Upregulated"

  • Downregulation is the process by which a cell decreases the production and quantities of its cellular components, such as RNA and proteins, in response to an external stimulus.
  • Upregulation is the complemetary process that involves increase in quantities of cellular components in response to an external stimulus.

• NAME: name of the file

• TYPE: indicates if the row belongs to a dataset of Enrichment or genes.

Genes Dataset:

There are 2 dataset of genes type, one called "MIGRASI_vs_MIGRANO" and one called "RISPOSTA_AL_FARMACO_SI_vs_RISPOSTA_AL_FARMACO_NO, both have same 16 columns.

• ROW.NAMES: Ensembl Transcript ID for transcript level results.

• BASEMEAN: The average of the normalized count values, dividing by size factors, taken over all samples.

• LOG2FOLDCHANGE: the effect size estimate. This value indicates how much the gene or transcript's expression seems to have changed between the comparison and control groups. This value is reported on a logarithmic scale to base 2.

• LFCSE: The standard error estimate for the log2 fold change estimate.

• STAT: The value of the test statistic for the gene or transcript.

• PVALUE: P-value of the test for the gene or transcript. A lower p-value suggests that it's unlikely the observed difference occurred by random chance.

• PADJ: Adjusted P-value for multiple testing for the gene or transcript.

• V1: ?

• V2: ?

• V3: ?

• V5: ? type of the gene

• V6: ?

• V7: gene nomenclature based on the id in row.names

• REGULATION: indicates the type of regulation of gene expression, it can be "Downregulated" or "Upregulated"

  • Downregulation is the process by which a cell decreases the production and quantities of its cellular components, such as RNA and proteins, in response to an external stimulus.
  • Upregulation is the complemetary process that involves increase in quantities of cellular components in response to an external stimulus.

• NAME: name of the file

• TYPE: indicates if the row belongs to a dataset of Enrichment or genes.

Resources

• https://geneontology.org/
• https://bioconductor.org/packages/release/bioc/html/DESeq2.html
• https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
• https://github.com/owkin/PyDESeq2
• https://www.uniprot.org/
• https://pantherdb.org/
• https://pydeseq2.readthedocs.io/en/latest/auto_examples/plot_minimal_pydeseq2_pipeline.html#sphx-glr-auto-examples-plot-minimal-pydeseq2-pipeline-py
• https://www.ebi.ac.uk/QuickGO/api/index.html#!/gene_ontology/findAncestorsUsingGET_1
• https://pubmed.ncbi.nlm.nih.gov/12539951/
• https://pubmed.ncbi.nlm.nih.gov/29145629/