Strategy-4

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

100 Positive Negative Protein Dataset used for Cutoff

dataset-100pos-neg-for-cutoff.xlsx

Cutoff for Vax-Elan pipeline tools

Cl Brener 19k Protein Original Dataset

Tcruzi_clbrener_final_files_with_vaxijen.xlsx

Cl Brener 19k Protein Binary Dataset

Binary_without_rowwisesum.xlsx

Sorted Cl Brener 19k Protein Binary Dataset with row-wise sum

Binary_with_rowwisesum.xlsx

Filtering Strategy

Cl Brener 19k Protein Top 100 Proteins after filtering

top100_19knew.xlsx

Strategy 4 used in Vax-Elan pipeline

T. cruzi CL Brener 19k Protein Distribution

19knewdistrib.docx

100 Positive Negative Protein Distribution

analysis_100_pos_neg.pdf

Cl Brener 19k-100 Positive Negative Protein Distribution

19k_posneg_distrib.docx

Top 100 proteins retrieved by Strategy-4

Top 8 unique proteins:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi strain CL Brener]


Top-100_Strategy-4.xlsx

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:-

Strategy-4:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]

Strategy-1:-

  1. XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_816522.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_821916.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_804513.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  7. XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]

  8. XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]

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:-

Strategy-4:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]

Strategy-2:-

  1. XP_809166.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_811700.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_822020.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_804447.1 ubiquitin-conjugating enzyme E2 [Trypanosoma cruzi strain CL Brener]

  5. XP_807999.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_806523.1 IgE-dependent histamine-releasing factor [Trypanosoma cruzi strain CL Brener]

  7. XP_808372.1 small nuclear ribonucleoprotein Sm-E [Trypanosoma cruzi strain CL Brener]

  8. XP_818708.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

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:-

Strategy-4:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]

Strategy-3:-

  1. XP_805056.1 mucin-associated surface protein (MASP) [Trypanosoma cruzi strain CL Brener]

  2. XP_802955.1 mucin TcMUCII [Trypanosoma cruzi strain CL Brener]

  3. XP_815016.1 90 kDa surface protein [Trypanosoma cruzi strain CL Brener]

  4. XP_807308.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_821176.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  6. XP_804140.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  7. XP_816111.1 subtilisin-like serine peptidase [Trypanosoma cruzi strain CL Brener]

  8. XP_806816.1 DnaJ chaperone protein [Trypanosoma cruzi strain CL Brener]

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:-

Strategy-4:-

  1. XP_816052.1 phosphate-repressible phosphate permease [Trypanosoma cruzi strain CL Brener]

  2. XP_807493.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  3. XP_803296.1 dispersed gene family protein 1 (DGF-1), partial [Trypanosoma cruzi strain CL Brener]

  4. XP_822017.1 trans-sialidase [Trypanosoma cruzi strain CL Brener]

  5. XP_819804.1 nucleoside transporter-like [Trypanosoma cruzi strain CL Brener]

  6. XP_820852.1 serine/threonine protein kinase [Trypanosoma cruzi strain CL Brener]

  7. XP_815460.1 receptor-type adenylate cyclase, partial [Trypanosoma cruzi strain CL Brener]

  8. XP_812509.1 UDP-N-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase [Trypanosoma cruzi CL Brener]

Strategy-5:-

  1. XP_809117.1 hypothetical protein [Trypanosoma cruzi strain CL Brener]

  2. XP_821990.1 mucin-associated surface protein (MASP [Trypanosoma cruzi strain CL Brener]

  3. RNC42421.1 mucin TcMUCII [Trypanosoma cruzi]

  4. XP_803883.1 GP85-like protein, partial [Trypanosoma cruzi strain CL Brener]

  5. AAL90889.1 Tcc1j12.3 [Trypanosoma cruzi]

  6. XP_809960.1 trans-sialidase [Trypanosoma cruzi strain CL brener]

  7. XP_808931.1 mucin TcMUCIII {Trypanosoma cruzi strain CL Brener]