Galaxy | ProteoRE | Published Workflow | Pancreatic_Cancer_Biomarkers_Selection (from Vandenbrouck et al., Proteomics 2020)

Pancreatic_Cancer_Biomarkers_Selection (from Vandenbrouck et al., Proteomics 2020)

Step	Annotation
Step 1: Build tissue-specific expression dataset Experimental data source (antibody- or RNAseq-based) RNA levels based on RNA-seq experiments HPA source files version tool-data/HPA_RNA_tissue_23-10-2018.tsv Select tissue (by clicking in the box) pancreas
Step 2: Build tissue-specific expression dataset Experimental data source (antibody- or RNAseq-based) Expression profiles based on immunohistochemistry HPA source files version tool-data/HPA_normal_tissue_23-10-2018.tsv Select tissue (by clicking in the box) pancreas Expression level High Medium Reliability score Enhanced Supported
Step 3: Input dataset Pancreas cancer transcriptome dataset (HPA) (rna_cancer_detectable_pancreatic.tsv) select at runtime
Step 4: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 1 Does file contain header? True Operation Keep Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by numerical values Filter by numerical value 1 Column number on which to apply the filter c4 Select operator >= Value 10.0 Filter by range of numerical values Sort by column ? True Sort result files by: c4 Sort in descending order ? False
Step 5: Venn diagram List to compares List to compare 1 Enter your list Input file containing your list Select your file Output dataset 'kept_lines' from step 4 Does file contain header? True Column number on which apply the comparison c1 Enter the name of this list Pancreas (RNAseq) List to compare 2 Enter your list Input file containing your list Select your file Output dataset 'output' from step 2 Does file contain header? True Column number on which apply the comparison c1 Enter the name of this list Pancreas (IHC) List to compare 3 Enter your list Input file containing your list Select your file Output dataset 'output' from step 3 Does file contain header? True Column number on which apply the comparison c3 Enter the name of this list PC (RNAseq)
Step 6: Cut File to cut Output dataset 'output_text' from step 5 Operation Keep Delimited by Tab Cut by fields List of Fields 6
Step 7: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 3 Does file contain header? True Operation Keep Select an operator to combine your filters (if more than one) AND Filter by keywords Filter by keywords 1 Column number on which to apply the filter c15 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) enhanced enriched Filter by keywords 2 Column number on which to apply the filter c3 Search for exact match? False Enter keywords File containing keywords File containing keywords Output dataset 'output' from step 6 Specify the column containing keywords c1 Does file contain header? True Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 8: ID Converter Enter IDs Input file containing IDs Select your file Output dataset 'kept_lines' from step 7 Does file contain header? True Column number of IDs to map c3 Species Human (Homo sapiens) Release tool-data/Human_id_mapping_08-01-2020.tsv Type/source of IDs Ensembl gene ID (e.g. ENSG00000166913) Target type: Target type of IDs you would like to map to neXtProt ID (e.g. NX_P31946) UniProt accession number (e.g. P31946) - reviewed entries only
Step 9: Add protein features Enter your IDs (neXtProt or UniProt; e.g. P05090 or NX_P05090) Input file containing your IDs Select your file Output dataset 'output' from step 8 Column IDs (e.g : Enter c1 for column n°1) c23 Does input file have header? True Type of IDs neXtProt IDs Select features (Physico-chemical, localization, disease infiormation): Select information to add to your list Protein Existence (evidence score from 1 to 5) Localization Subcellular Location Disease information True Release of neXtProt reference file to use tool-data/nextprot_ref_07-05-2019.tsv
Step 10: Venn diagram List to compares List to compare 1 Enter your list Input file containing your list Select your file Output dataset 'output' from step 9 Does file contain header? True Column number on which apply the comparison c24 Enter the name of this list Candidate biomarkers List to compare 2 Enter your list Copy/paste list Copy/paste list A0AV02 A0FGR9 A0PJK1 A0PK11 A0ZSE6 A1A5B4 A1A5C7 A1L157 A2RRL7 A2VDJ0 A3KFT3 A4D2G3 A4IF30 A5X5Y0 A6BM72 A6H8M9 A6NC51 A6NCV1 A6ND01 A6ND48 A6NDA9 A6NDH6 A6NDL8 A6NDP7 A6NDV4 A6NET4 A6NF34 A6NF89 A6NFA1 A6NFC5 A6NFX1 A6NGU5 A6NGY5 A6NH00 A6NH21 A6NHA9 A6NHG9 A6NHS7 A6NI73 A6NIJ9 A6NIM6 A6NJW9 A6NJZ3 A6NK97 A6NKB5 A6NKC4 A6NKK0 A6NL08 A6NL26 A6NL88 A6NM03 A6NM11 A6NM45 A6NM76 A6NMB1 A6NMS3 A6NMS7 A6NMU1 A6NMZ5 A6NND4 A6NNN8 A7MBM2 A8MPY1 A8MUP6 A8MVS5 A8MVW0 A8MVW5 A8MVZ5 A8MWY0 A8MXK1 B0FP48 B2RN74 B3SHH9 B4DS77 B6A8C7 B6SEH8 B6SEH9 B8ZZ34 D3W0D1 E2RYF6 F2Z333 F5H4A9 G3V0H7 H3BS89 I3L273 O00144 O00155 O00206 O00220 O00222 O00241 O00254 O00270 O00322 O00337 O00341 O00391 O00398 O00400 O00421 O00451 O00478 O00481 O00526 O00533 O00548 O00574 O00590 O00591 O00592 O14493 O14494 O14495 O14511 O14514 O14522 O14524 O14525 O14581 O14626 O14672 O14718 O14764 O14786 O14788 O14798 O14804 O14817 O14836 O14842 O14843 O14894 O14917 O14931 O14944 O15031 O15118 O15146 O15165 O15197 O15218 O15244 O15245 O15303 O15321 O15354 O15374 O15375 O15389 O15394 O15399 O15403 O15431 O15438 O15439 O15440 O15455 O15529 O15547 O15551 O15552 O42043 O43155 O43157 O43184 O43193 O43194 O43246 O43280 O43291 O43300 O43306 O43315 O43424 O43490 O43493 O43497 O43506 O43511 O43556 O43567 O43570 O43603 O43613 O43614 O43653 O43657 O43688 O43699 O43749 O43826 O43868 O43869 O43895 O43921 O43934 O60235 O60241 O60242 O60245 O60266 O60279 O60309 O60330 O60353 O60359 O60391 O60403 O60404 O60412 O60431 O60449 O60462 O60469 O60478 O60486 O60487 O60500 O60503 O60602 O60603 O60609 O60635 O60636 O60637 O60669 O60706 O60755 O60779 O60883 O60895 O60896 O60931 O60939 O71037 O75015 O75019 O75022 O75023 O75051 O75054 O75074 O75077 O75078 O75084 O75096 O75121 O75129 O75144 O75197 O75309 O75311 O75325 O75326 O75355 O75387 O75388 O75443 O75445 O75473 O75487 O75508 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P16581 P16671 P16871 P17181 P17301 P17302 P17342 P17643 P17693 P17787 P17813 P17927 P17948 P18084 P18089 P18433 P18462 P18463 P18464 P18465 P18505 P18507 P18564 P18627 P18825 P18827 P19021 P19022 P19075 P19235 P19256 P19320 P19397 P19438 P19440 P19634 P20023 P20036 P20039 P20138 P20273 P20309 P20333 P20594 P20645 P20701 P20702 P20827 P20916 P21439 P21452 P21453 P21462 P21554 P21583 P21589 P21709 P21728 P21730 P21731 P21754 P21757 P21802 P21860 P21917 P21918 P21926 P22001 P22223 P22303 P22413 P22455 P22607 P22732 P22748 P22794 P22888 P22897 P23229 P23276 P23415 P23416 P23467 P23468 P23470 P23471 P23510 P23515 P23634 P23942 P23945 P23975 P24046 P24071 P24394 P24530 P25021 P25024 P25025 P25063 P25089 P25090 P25092 P25100 P25101 P25103 P25105 P25106 P25116 P25189 P25445 P25929 P25942 P26006 P26010 P26012 P26715 P26717 P26718 P26842 P26951 P26992 P27037 P27487 P27701 P27930 P28067 P28068 P28221 P28222 P28223 P28335 P28336 P28472 P28476 P28566 P28827 P28906 P28907 P28908 P29016 P29017 P29033 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Q5TFQ8 Q5TZ20 Q5UAW9 Q5VT99 Q5VU13 Q5VU65 Q5VU97 Q5VUB5 Q5VV43 Q5VV63 Q5VW38 Q5VWK5 Q5VX71 Q5VXU1 Q5VY43 Q5VY80 Q5VYJ5 Q5VZ72 Q5XXA6 Q5Y7A7 Q5ZPR3 Q685J3 Q687X5 Q68D85 Q68DH5 Q68DV7 Q69384 Q695T7 Q6DN72 Q6DWJ6 Q6EMK4 Q6GTX8 Q6GV28 Q6H3X3 Q6IA17 Q6ICI0 Q6IEE7 Q6IEU7 Q6IEV9 Q6IEY1 Q6IEZ7 Q6IF00 Q6IF42 Q6IF63 Q6IF82 Q6IF99 Q6IFG1 Q6IFH4 Q6IFN5 Q6ISU1 Q6IWH7 Q6J4K2 Q6MZM0 Q6N022 Q6N075 Q6NUJ2 Q6NUS6 Q6NUT3 Q6NV75 Q6NVV3 Q6NW40 Q6P1J6 Q6P499 Q6P4Q7 Q6P5W5 Q6P995 Q6P9G4 Q6PCB8 Q6PEY0 Q6PI73 Q6PIZ9 Q6PJF5 Q6PJG9 Q6PRD1 Q6PXP3 Q6Q8B3 Q6QNK2 Q6T423 Q6U736 Q6U841 Q6UQ28 Q6UVK1 Q6UW56 Q6UW88 Q6UWB1 Q6UWI2 Q6UWJ1 Q6UWJ8 Q6UWL2 Q6UWL6 Q6UWN0 Q6UWN5 Q6UWR7 Q6UWV2 Q6UX01 Q6UX15 Q6UX27 Q6UX71 Q6UX82 Q6UXB3 Q6UXB4 Q6UXB8 Q6UXC1 Q6UXD5 Q6UXD7 Q6UXE8 Q6UXF1 Q6UXG2 Q6UXG3 Q6UXG8 Q6UXK2 Q6UXK5 Q6UXL0 Q6UXM1 Q6UXN8 Q6UXU4 Q6UXV0 Q6UXZ0 Q6UXZ3 Q6UXZ4 Q6UY09 Q6UY11 Q6UY18 Q6V0I7 Q6V1P9 Q6W5P4 Q6YBV0 Q6YHK3 Q6ZMB5 Q6ZMC9 Q6ZMD2 Q6ZMH5 Q6ZMI3 Q6ZMJ2 Q6ZN44 Q6ZNA5 Q6ZP29 Q6ZP80 Q6ZQN7 Q6ZRH7 Q6ZRP7 Q6ZS10 Q6ZSJ9 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Q9UGT4 Q9UHC6 Q9UHC9 Q9UHF4 Q9UHI7 Q9UHM6 Q9UHP7 Q9UHW9 Q9UHX3 Q9UI33 Q9UI40 Q9UIB8 Q9UIG8 Q9UIK5 Q9UIQ6 Q9UIW2 Q9UJ14 Q9UJ42 Q9UJ99 Q9UJA9 Q9UJQ1 Q9UK23 Q9UKB5 Q9UKF2 Q9UKF5 Q9UKG4 Q9UKH3 Q9UKJ0 Q9UKJ1 Q9UKJ8 Q9UKL2 Q9UKL4 Q9UKN1 Q9UKP6 Q9UKQ2 Q9UKU6 Q9UKX5 Q9UKY0 Q9UKZ4 Q9UL52 Q9ULB1 Q9ULB4 Q9ULB5 Q9ULC0 Q9ULF5 Q9ULH4 Q9ULI3 Q9ULK0 Q9ULK6 Q9ULL4 Q9ULQ1 Q9ULV1 Q9ULW2 Q9ULX7 Q9ULZ9 Q9UM44 Q9UM47 Q9UM73 Q9UMF0 Q9UMX9 Q9UMZ3 Q9UN42 Q9UN66 Q9UN67 Q9UN70 Q9UN71 Q9UN72 Q9UN73 Q9UN74 Q9UN75 Q9UN76 Q9UN88 Q9UNE0 Q9UNG2 Q9UNN8 Q9UNQ0 Q9UNW8 Q9UP38 Q9UP95 Q9UPC5 Q9UPI3 Q9UPR5 Q9UPU3 Q9UPX0 Q9UPZ6 Q9UQ52 Q9UQC9 Q9UQD0 Q9UQF0 Q9UQQ1 Q9UQV4 Q9Y219 Q9Y226 Q9Y267 Q9Y271 Q9Y275 Q9Y286 Q9Y287 Q9Y289 Q9Y2C9 Q9Y2I2 Q9Y2T5 Q9Y2T6 Q9Y336 Q9Y345 Q9Y3B3 Q9Y3N9 Q9Y3P8 Q9Y3Q7 Q9Y487 Q9Y493 Q9Y4A9 Q9Y4C0 Q9Y4D2 Q9Y4D7 Q9Y561 Q9Y585 Q9Y5E1 Q9Y5E2 Q9Y5E3 Q9Y5E4 Q9Y5E5 Q9Y5E6 Q9Y5E7 Q9Y5E8 Q9Y5E9 Q9Y5F0 Q9Y5F1 Q9Y5F2 Q9Y5F3 Q9Y5F6 Q9Y5F7 Q9Y5F8 Q9Y5F9 Q9Y5G0 Q9Y5G1 Q9Y5G2 Q9Y5G3 Q9Y5G4 Q9Y5G5 Q9Y5G6 Q9Y5G7 Q9Y5G8 Q9Y5G9 Q9Y5H0 Q9Y5H1 Q9Y5H2 Q9Y5H3 Q9Y5H4 Q9Y5H5 Q9Y5H6 Q9Y5H7 Q9Y5H8 Q9Y5H9 Q9Y5I0 Q9Y5I1 Q9Y5I2 Q9Y5I3 Q9Y5I4 Q9Y5I7 Q9Y5N1 Q9Y5P0 Q9Y5P1 Q9Y5Q5 Q9Y5S1 Q9Y5U5 Q9Y5X5 Q9Y5Y0 Q9Y5Y3 Q9Y5Y4 Q9Y5Y7 Q9Y5Y9 Q9Y5Z0 Q9Y624 Q9Y625 Q9Y639 Q9Y653 Q9Y666 Q9Y691 Q9Y694 Q9Y698 Q9Y6F6 Q9Y6H8 Q9Y6L6 Q9Y6M0 Q9Y6M5 Q9Y6M7 Q9Y6N7 Q9Y6N8 Q9Y6Q6 Q9Y6R1 Q9Y6W8 Q9Y6X5 Enter the name of this list Human surfaceome
Step 11: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 9 Does file contain header? True Operation Keep Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by keywords 1 Column number on which to apply the filter c26 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) Secretory Secreted Extracellular Apical Basolateral junction Filter by keywords 2 Column number on which to apply the filter c24 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) O94778 Q9Y6R1 P16444 Q07837 Q86UP6 P19075 P55259 Filter by numerical values Filter by range of numerical values Sort by column ? True Sort result files by: c1 Sort in descending order ? False
Step 12: Get MS/MS observations in tissue/fluid Enter your IDs (UniProt Accession number only) Input file containing your IDs Select your file Output dataset 'kept_lines' from step 11 Does file contain header? True Column of IDs c24 Proteomics dataset (biological sample) tool-data/Human_Plasma_non_glyco_2017-04.tsv
Step 13: Filter by keywords and/or numerical value Input file Output dataset 'output' from step 12 Does file contain header? True Operation Discard Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by keywords 1 Column number on which to apply the filter c28 Search for exact match? True Enter keywords copy/paste Copy/paste keywords to find (keep or discard) NA Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 14: Get expression profiles Enter your IDs (Ensembl gene ID only; e.g. ENSG00000163631) Input file containing your IDs file Output dataset 'kept_lines' from step 13 Does file contain header? True Column number of IDs to map c3 Human Protein Atlas (normal or tumor tissue) Human Normal Tissue Normal tissue HPA version 18.1 tool-data/HPA_normal_tissue_23-10-2018.tsv Select tissue(s) Pancreas Expression level High Medium Reliability score Enhanced Supported Keep IDs not found in HPA? True
Step 15: Venn diagram List to compares List to compare 1 Enter your list Input file containing your list Select your file Output dataset 'kept_lines' from step 13 Does file contain header? True Column number on which apply the comparison c24 Enter the name of this list Candidate biomarkers List to compare 2 Enter your list Copy/paste list Copy/paste list O95994 P04003 P01031 Q8WXI7 Q969X2 P07339 P16144 P16070 P12109 O14625 P51671 P16422 P54753 O15520 Q14956 P14210 P05362 Q14773 P05019 P18065 P22301 P05231 P10145 P12268 P02778 Q13753 P07195 P02750 P08581 Q99988 P39900 P09237 P98088 Q6UX06 O00300 P13725 P01127 P04085 P01833 P02775 P07478 P48304 P21583 Q0VAF6 P10646 P35442 P01033 P19075 Q9BZM5 Enter the name of this list Biomarkers from literature
Step 16: Filter by keywords and/or numerical value Input file Output dataset 'hpa_output' from step 14 Does file contain header? True Operation Keep Select an operator to combine your filters (if more than one) OR Filter by keywords Filter by keywords 1 Column number on which to apply the filter c4 Search for exact match? False Enter keywords copy/paste Copy/paste keywords to find (keep or discard) exocrine Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 17: Filter by keywords and/or numerical value Input file Output dataset 'kept_lines' from step 13 Does file contain header? True Operation Keep Select an operator to combine your filters (if more than one) AND Filter by keywords Filter by keywords 1 Column number on which to apply the filter c3 Search for exact match? False Enter keywords File containing keywords File containing keywords Output dataset 'kept_lines' from step 16 Specify the column containing keywords c1 Does file contain header? True Filter by keywords 2 Column number on which to apply the filter c27 Search for exact match? True Enter keywords copy/paste Copy/paste keywords to find (keep or discard) NA Filter by numerical values Filter by range of numerical values Sort by column ? False
Step 18: Get unique peptide SRM-MRM method Enter IDs (Uniprot Accession number, e.g. P04746) Input file containing Uniprot-AC identifiers Select your file Output dataset 'kept_lines' from step 17 Does file contain header? True Column number of IDs c24 Release tool-data/Human_SRM_atlas_2016-04.csv Peptide sequence/features Peptide sequence SSRT (Sequence Specific Retention Time) Length (peptide sequence length) MW (Molecular weight) PeptideAtlas Accession (PA_Acc)

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