Embedded Files
It includes the conversion of T.cruzi CL Brener (19,602) final file into a binary file and ranking them on order the threshold values.
It includes the conversion of T.cruzi CL Brener (19,602) final file into a binary file and ranking them on order the threshold values.
Following are the attached snapshots demonstrating the logic behind converting 19602*21 features and the files containing python script used for conversion and their outputs. It contains the source file(original 19k ) which was changed to binary using derived thresholds and their sum across the rows with their ranking score. It also contains top 100 and bottom 100 features files.
Cutoff Strategy
Cutoff Strategy
100 Positive Negative Protein Dataset used for Cutoff
100 Positive Negative Protein Dataset used for Cutoff
dataset-100pos-neg-for-cutoff.xlsxCutoff for Vax-Elan pipeline tools
Cutoff for Vax-Elan pipeline tools
Cl Brener 19k Protein Original Dataset
Cl Brener 19k Protein Original Dataset
Tcruzi_clbrener_final_files_with_vaxijen.xlsxCl Brener 19k Protein Binary Dataset
Cl Brener 19k Protein Binary Dataset
Binary_without_rowwisesum.xlsxSorted Cl Brener 19k Protein Binary Dataset with row-wise sum
Sorted Cl Brener 19k Protein Binary Dataset with row-wise sum
Binary_with_rowwisesum.xlsxFiltering Strategy
Filtering Strategy
Cl Brener 19k Protein Top 100 Proteins after filtering
Cl Brener 19k Protein Top 100 Proteins after filtering
top100_19knew.xlsxStrategy 4 used in Vax-Elan pipeline
T. cruzi CL Brener 19k Protein Distribution
T. cruzi CL Brener 19k Protein Distribution
19knewdistrib.docx100 Positive Negative Protein Distribution
100 Positive Negative Protein Distribution
analysis_100_pos_neg.pdfCl Brener 19k-100 Positive Negative Protein Distribution
Cl Brener 19k-100 Positive Negative Protein Distribution
19k_posneg_distrib.docxTop 100 proteins retrieved by Strategy-4
Top 100 proteins retrieved by Strategy-4
Top 8 unique proteins:-
Top 8 unique proteins:-
XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]
XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]
XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]
XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]
XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi strain CL Brener]
Top-100_Strategy-4.xlsxStrategy-4 vs Strategy-1
Strategy-4 vs Strategy-1
No intersection of proteins were found upon filtering of proteins via Strategy-4 and Strategy-1.
Union of proteins in Strategy-4 and Strategy-1:-
Union of proteins in Strategy-4 and Strategy-1:-
Strategy-4:-
XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]
XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]
XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]
XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]
XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]
Strategy-1:-
XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]
XP_816522.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]
XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]
XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_821916.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_804513.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]
XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]
Strategy-4 vs Strategy-2
Strategy-4 vs Strategy-2
No intersection of proteins were found upon filtering of proteins via Strategy-4 and Strategy-2.
Union of proteins in Strategy-4 and Strategy-2:-
Union of proteins in Strategy-4 and Strategy-2:-
Strategy-4:-
XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]
XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]
XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]
XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]
XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]
Strategy-2:-
XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]
XP_811700.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]
XP_822020.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]
XP_804447.1 ubiquitin-conjugating enzyme E2 [Trypanosoma cruzi strain CL Brener]
XP_807999.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_806523.1 IgE-dependent histamine-releasing factor [Trypanosoma cruzi strain CL Brener]
XP_808372.1 small nuclear ribonucleoprotein Sm-E [Trypanosoma cruzi strain CL Brener]
XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
Strategy-4 vs Strategy-3
Strategy-4 vs Strategy-3
No intersection of proteins were found upon filtering of proteins via Strategy-4 and Strategy-3.
Union of proteins in Strategy-4 and Strategy-3:-
Union of proteins in Strategy-4 and Strategy-3:-
Strategy-4:-
XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]
XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]
XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]
XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]
XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]
Strategy-3:-
XP_805056.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]
XP_802955.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]
XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]
XP_807308.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_821176.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_804140.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]
XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]
Strategy-4 vs Strategy-5
Strategy-4 vs Strategy-5
No intersection of proteins were found upon filtering of proteins via Strategy-4 and Strategy-5.
Union of proteins in Strategy-4 and Strategy-5:-
Union of proteins in Strategy-4 and Strategy-5:-
Strategy-4:-
XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]
XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]
XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]
XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]
XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]
XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]
XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]
Strategy-5:-
XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]
XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]
RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]
XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]
AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]
XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]
XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]
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