/// <summary>
/// Author: Ryan Liang
/// </summary>
private void CreateSNVIdentificationTable(SNV_Mutation mutation)
{
TableHeaderRow tableHeaderRow = new TableHeaderRow {
TableSection = TableRowSection.TableHeader
};
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Variant ID"
});
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "SNV"
});
tableHeaderRow.Cells.Add(new TableHeaderCell {
Text = "Predicted Effect on Drug Binding"
});
SNV_Identification_Table.Rows.Add(tableHeaderRow);
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P1W, mutation.SNV_P1W_ID, mutation.Drug_Inter__Pred__P1W));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P2W, mutation.SNV_P2W_ID, mutation.Drug_Inter__Pred__P2W));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P3W, mutation.SNV_P3W_ID, mutation.Drug_Inter__Pred__P3W));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P1M1, mutation.SNV_P1M1_ID, mutation.Drug_Inter__Pred__P1M1));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P1M2, mutation.SNV_P1M2_ID, mutation.Drug_Inter__Pred__P1M2));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P1M3, mutation.SNV_P1M3_ID, mutation.Drug_Inter__Pred__P1M3));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P2M1, mutation.SNV_P2M1_ID, mutation.Drug_Inter__Pred__P2M1));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P2M2, mutation.SNV_P2M2_ID, mutation.Drug_Inter__Pred__P2M2));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P2M3, mutation.SNV_P2M3_ID, mutation.Drug_Inter__Pred__P2M3));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P3M1, mutation.SNV_P3M1_ID, mutation.Drug_Inter__Pred__P3M1));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P3M2, mutation.SNV_P3M2_ID, mutation.Drug_Inter__Pred__P3M2));
SNV_Identification_Table.Rows.Add(CreateSNVIDTableRow(mutation.P3M3, mutation.SNV_P3M3_ID, mutation.Drug_Inter__Pred__P3M3));
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private void LoadTargetGeneID(Protein_Information protein, SNV_Mutation mutation)
{
ProcessRow(gene_name_row, gene_name, mutation.NCBI_Gene_Name);
ProcessRow(uniprot_id_row, uniprot_id, protein.UniProt_ID);
ProcessRow(ncbi_refseq_id_row, ncbi_refseq_id, protein.NCBI_RefSeq_NP_ID);
ProcessRow(chromosome_location_row, chromosome_location, protein.Human_Chromosome_Location);
gene_and_protein_info_url.Text = "Link to further gene and protein information";
gene_and_protein_info_url.NavigateUrl = "ProteinInfoResult.aspx?query_string=" + protein.UniProt_ID;
gene_and_protein_info_url.Target = "_blank";
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static SNV_Mutation GetMutationBySNVKey(string SNV_Key)
{
SNV_Mutation SNV_mutation = new SNV_Mutation();
using (DrugProNETEntities context = new DrugProNETEntities())
{
SNV_mutation = context.SNV_Mutation.Where(m => m.SNV_Key.Equals(SNV_Key, StringComparison.OrdinalIgnoreCase)).SingleOrDefault();
}
return(SNV_mutation);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadDrug(Drug_Information drug, SNV_Mutation mutation)
{
ProcessRow(PDB_drug_ID_row, PDB_drug_ID, mutation.Drug_PDB_ID, drug.Drug_PDB_ID_URL);
ProcessRow(drug_name_row, drug_name, drug.Drug_Common_Name);
ProcessRow(pubchem_cid_row, pubchem_cid, drug.PubChem_CID, drug.PubChem_Compound_Link);
ProcessRow(chembl_id_row, chembl_id, drug.ChEMBL_ID, drug.ChEMBL_Link);
ProcessRow(chemspider_id_row, chemspider_id, drug.ChemSpider_ID, drug.ChemSpider_Link);
ProcessRow(drugbank_id_row, drugbank_id, drug.DrugBank_ID, drug.DrugBank_Link);
ProcessRow(drug_information_result_url_row, drug_information_result_url, "Click here for more drug information from DrugProNET",
"DrugInfoResult.aspx?query_string=" + drug.Drug_Name_for_Pull_Down_Menu);
}
/// <summary>
/// Author: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
SNV_ID_Key = Request.QueryString["query_string"];
try
{
string stringAfterPDot = SNV_ID_Key.Substring(SNV_ID_Key.IndexOf("p.") + 2);
string specifiedAAType = new string(stringAfterPDot.TakeWhile(c => char.IsLetter(c)).ToArray());
string specifiedAANumber = new string(stringAfterPDot.Substring(specifiedAAType.Length).TakeWhile(c => char.IsNumber(c)).ToArray());
string specifiedAA = specifiedAAType + "-" + specifiedAANumber;
mutations = EF_Data.GetMutationsBySNVIDKey(SNV_ID_Key);
proteinMutation = EF_Data.GetMutationBySNVIDKey(SNV_ID_Key);
protein = EF_Data.GetProteinByUniprotID(proteinMutation.UniProt_ID);
foreach (SNV_Mutation mutation in mutations)
{
Drug_Information drug = EF_Data.GetDrugByDrugPDBID(mutation.Drug_PDB_ID);
drugs.Add(drug);
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(mutation.UniProt_ID, mutation.Drug_PDB_ID, specifiedAA);
interactions.Add(interaction);
}
Session["drugs"] = drugs;
Session["interactions"] = interactions;
Session["mutations"] = mutations;
Session["SNV_ID_Key"] = SNV_ID_Key;
LoadSNVID(SNV_ID_Key);
LoadTargetGeneID(protein, mutations[0]);
CreateIDofPDILinkedSNVTable(drugs, interactions, mutations);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private string FindPredictedEffiency(SNV_Mutation mutation)
{
if (mutation.SNV_P1M1_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P1M1);
}
else if (mutation.SNV_P1M2_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P1M2);
}
else if (mutation.SNV_P1M3_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P1M3);
}
else if (mutation.SNV_P2M1_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P2M1);
}
else if (mutation.SNV_P2M2_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P2M2);
}
else if (mutation.SNV_P2M3_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P2M3);
}
else if (mutation.SNV_P3M1_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P3M1);
}
else if (mutation.SNV_P3M2_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P3M2);
}
else if (mutation.SNV_P3M3_ID.Equals(SNV_ID_Key, StringComparison.OrdinalIgnoreCase))
{
return(mutation.Drug_Inter__Pred__P3M3);
}
return(null);
}
/// <summary>
/// Author: Garth Nelson
/// </summary>
protected new void Page_Load(object sender, EventArgs e)
{
base.Page_Load(sender, e);
try
{
string protein_specification = Request.QueryString["query_string"];
string drug_specification = Request.QueryString["drug_specification"];
string SNV_Key = Request.QueryString["snv_id_key"];
Session["SNV_Key"] = SNV_Key;
Protein_Information protein = EF_Data.GetProtein(protein_specification);
Drug_Information drug = EF_Data.GetDrugUsingDropDownName(drug_specification);
PDB_Information PDB = EF_Data.GetPDBInfo(protein, drug);
string[] SNV_KEYsplit = SNV_Key.Split('-');
// Retrieve second and third elements
string amino_acid_specification = SNV_KEYsplit[1] + "-" + SNV_KEYsplit[2];
PDB_Interaction interaction = EF_Data.GetPDB_Interaction(protein.Uniprot_ID, drug.Drug_PDB_ID, amino_acid_specification);
mutation = EF_Data.GetMutationBySNVKey(SNV_Key);
Session["mutation"] = mutation;
LoadProtein(protein, interaction, mutation);
LoadDrug(drug, mutation);
LoadPDB_Info(PDB);
CreateSNVIdentificationTable(mutation);
}
catch (Exception)
{
Page.Master.FindControl("BodyContentPlaceHolder").Visible = false;
ExceptionUtilities.DisplayAlert(this, QUERY_PAGE);
}
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
private TableRow CreateTableRow(Drug_Information drug, PDB_Interaction interaction, SNV_Mutation mutation)
{
TableRow tableRow = new TableRow();
tableRow.Cells.Add(new TableCell()
{
Text = drug.Drug_Common_Name
});
tableRow.Cells.Add(new TableCell()
{
Text = mutation.PDB_File_ID
});
tableRow.Cells.Add(new TableCell()
{
Text = mutation.Drug_PDB_ID
});
tableRow.Cells.Add(new TableCell()
{
Text = drug.PubChem_CID
});
tableRow.Cells.Add(new TableCell()
{
Text = drug.ChEMBL_ID
});
if (double.TryParse(interaction?.Interaction_Distance_Ratio, out double result))
{
tableRow.Cells.Add(new TableCell()
{
Text = result.ToString("0.0")
});
}
else
{
tableRow.Cells.Add(new TableCell()
{
Text = ""
});
}
string predictedEffiency = FindPredictedEffiency(mutation);
tableRow.Cells.Add(new TableCell()
{
Text = predictedEffiency
});
return(tableRow);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public void LoadProtein(Protein_Information protein, PDB_Interaction interaction, SNV_Mutation mutation)
{
ProcessRow(gene_name_row, gene_name, mutation.NCBI_Gene_Name);
ProcessRow(uniprot_id_row, uniprot_id, mutation.UniProt_ID, protein.UniProt_Entry_URL);
ProcessRow(refseq_id_row, refseq_id, protein.NCBI_RefSeq_NP_ID, protein.NCBI_RefSeq_NP_ID_URL);
ProcessRow(nucleotide_id_row, nucleotide_id, protein.NCBI_Nucleotide_ID, protein.NCBI_Nucleotide_ID_URL);
ProcessRow(gene_id_row, gene_id, protein.NCBI_Gene_ID, protein.NCBI_Gene_URL);
ProcessRow(chromosome_location_row, chromosome_location, protein.Human_Chromosome_Location);
ProcessRow(gene_location_row, gene_location, protein.Human_Gene_Location);
ProcessRow(aa_residue_no_row, aa_residue_no, interaction.Uniprot_Residue_Number);
ProcessRow(atomic_interactions_row, atomic_interactions, interaction.Number_of_Atomic_Interactions);
ProcessRow(aa_residue_type_row, aa_residue_type, interaction.AA_Residue_Type);
ProcessRow(avg_atom_distance_row, avg_atom_distance, interaction.Average_Distance_Between_Atoms);
ProcessRow(interaction_distance_ratio_row, interaction_distance_ratio, interaction.Interaction_Distance_Ratio);
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
protected void Download_SNV_Identification_Click(object sender, EventArgs e)
{
Response.ClearContent();
Response.Clear();
Response.ContentType = "application/x-unknown";
Response.AddHeader("Content-Disposition", "attachment; " +
"filename=DrugProNET_SNV " + Session["SNV_Key"] + ".xlsx");
mutation = (SNV_Mutation)Session["mutation"];
List <string> header = new List <string>()
{
"Variant ID", "SNV", "Predicted Effect on Drug Binding"
};
List <List <string> > data = new List <List <string> >()
{
new List <string>()
{
mutation.P1W, mutation.SNV_P1W_ID, mutation.Drug_Inter__Pred__P1W
},
new List <string>()
{
mutation.P2W, mutation.SNV_P2W_ID, mutation.Drug_Inter__Pred__P2W
},
new List <string>()
{
mutation.P3W, mutation.SNV_P3W_ID, mutation.Drug_Inter__Pred__P3W
},
new List <string>()
{
mutation.P1M1, mutation.SNV_P1M1_ID, mutation.Drug_Inter__Pred__P1M1
},
new List <string>()
{
mutation.P1M2, mutation.SNV_P1M2_ID, mutation.Drug_Inter__Pred__P1M2
},
new List <string>()
{
mutation.P1M3, mutation.SNV_P1M3_ID, mutation.Drug_Inter__Pred__P1M3
},
new List <string>()
{
mutation.P2M1, mutation.SNV_P2M1_ID, mutation.Drug_Inter__Pred__P2M1
},
new List <string>()
{
mutation.P2M2, mutation.SNV_P2M2_ID, mutation.Drug_Inter__Pred__P2M2
},
new List <string>()
{
mutation.P2M3, mutation.SNV_P2M3_ID, mutation.Drug_Inter__Pred__P2M3
},
new List <string>()
{
mutation.P3M1, mutation.SNV_P3M1_ID, mutation.Drug_Inter__Pred__P3M1
},
new List <string>()
{
mutation.P3M2, mutation.SNV_P3M2_ID, mutation.Drug_Inter__Pred__P3M2
},
new List <string>()
{
mutation.P3M3, mutation.SNV_P3M3_ID, mutation.Drug_Inter__Pred__P3M3
},
};
Response.BinaryWrite(ExcelWriter.CreateAsStream(header, data).ToArray());
Response.Flush();
Response.SuppressContent = true;
System.Web.HttpContext.Current.ApplicationInstance.CompleteRequest();
}
/// <summary>
/// Author: Ryan Liang
/// </summary>
public static SNV_Mutation GetMutationBySNVIDKey(string SNV_ID_Key)
{
SNV_Mutation SNV_mutation = GetMutationsBySNVIDKey(SNV_ID_Key).First();
return(SNV_mutation);
}
