Output format



DESCRIPTION


The prediction output for each peptide pair consists of the following columns:

  • HLA allele Allele name

  • Normal peptide Peptide from reference corresponding to the mutant peptide.

  • Normal MHC affinity Predicted binding affinity of normal peptide in nanoMolar units.

  • Normal MHC % rank %Rank of prediction score for nomal peptides.

  • Mutant peptide The extracted mutant peptide.

  • Mutant MHC affinity Predicted binding affinity of mutant peptide in nanoMolar units.

  • Mutant MHC % rank %Rank of prediction score for mutant peptides.

  • Gene ID Ensembl gene ID

  • Transcript ID Ensembl transcript ID

  • Amino acid change Amino acid change annotated in VEP file.

  • Allele Frequency Genomic mutant allele frequency detected by MuTect2.

  • Mismatches Number of mismatches between normal and mutant peptide.

  • Peptide position Position of amino acid change in the peptide. Can be a range in the case of insertions and frameshifts.

  • Chr Chromosome annotated in the VEP file.

  • Genomic position genome nucleotide position annotated in the VEP file.

  • Protein position amino acid position annotated in the VEP file.

  • Mutation consequence the consequence annotated in the VEP file translated into single-letter abbrevations:

      M: Missense variant

      I: Inframe insertion

      D: Inframe deletion

      F: Frameshift variant

  • Gene symbol HUGO symbol corresponding to the Ensembl gene ID.

  • Cancer driver gene Yes if the HUGO symbol is in the COSMIC reference list, No if it is not.

  • Expression Level Expression of the transcript which the mutant peptide was extracted from.

  • Mutant affinity score Calculated binding affinity score of the mutant peptide, based on a negative logistic function of the mutant MHC %Rank score. This is used to calculate the final prioritization score.

  • Normal affinity score Calculated binding affinity score of the normal peptide, based on a positive logistic function of the normal MHC %Rank score. This is used to calculate the final prioritization score.

  • Expression score Calculated expression score of the transcript expression level. This is used to calculate the final prioritization score.

  • Priority score calculated prioritization dependent on HLA binding affinity of mutant and normal peptides, gene expression, and allele frequency.


NetMHCpan output

%Rank of prediction score to a set of 200.000 random natural 9mer peptides. For more information go to NetMHCpan3.0 output format.




EXAMPLE OUTPUT

.mupexi file

# VERSION:	MuPeXI 1.1
# CALL:		/usr/cbs/bio/src/MuPeXI-1.1/mupexi/MuPeXI.py -c /usr/cbs/bio/src/MuPeXI-1.1/config.ini -w -m -v /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.0 -e /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.1 -a HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03 -l 9
# DATE:		Monday 15 of August 2016
# TIME:		15:34:35
# PWD:		/net/athena/usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7
HLA_allele	Norm_peptide	Norm_MHCAffinity	Norm_MHCrank	Mut_peptide	Mut_MHCAffinity	Mut_MHCrank	Gene_ID	Transcript_ID	Amino_Acid_Change	Allele_Frequency	Mismatches	peptide_position	Chr	Genomic_Position	Protein_position	Mutation_Consequence	Gene_Symbol	Cancer_Driver_Gene	Expression_Level	Mutant_affinity_score	Normal_affinity_score	Expression_score	priority_Score
HLA-B07:02	.L.......	13351.1	9.5	SPDLGGSKF	267.2	0.7	ENSG00000156510	ENST00000354624	L/P	0.784	1	2	10	69232785	83	M	HKDC1	No	61.0165798	0.998498817743263	5.175555005801869e-17	1.0	78
HLA-A02:01	.R.R...D.	26906.1	32.0	KMYLKIVEV	8.7	0.1	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9999251537724895	7.175095973164411e-66	0.9841444919059494	64
HLA-C03:03	G......G.	5847.9	6.0	FSVIVCHKM	272.0	0.8	ENSG00000048028	ENST00000003302	FQ/X	0.650	2	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9975273768433653	2.0611536181902037e-09	0.9841444919059494	64
HLA-C07:02	A.I..E...	5100.7	4.0	MYLKIVEVI	1136.8	0.8	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9975273768433653	4.5397868702434395e-05	0.9841444919059494	64
HLA-A31:01	T...N....	3096.9	6.0	KIVEVIQKR	99.7	0.9	ENSG00000048028	ENST00000003302	FQ/X	0.650	2	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.995929862284104	2.0611536181902037e-09	0.9841444919059494	64
HLA-C03:03	.....G.VY	4781.8	5.0	VIVCHKMYL	643.9	1.4	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9525741268224334	3.059022269256247e-07	0.9841444919059494	61
HLA-A31:01	......DP.	1025.1	3.5	LFSVIVCHK	214.0	1.4	ENSG00000048028	ENST00000003302	FQ/X	0.650	2	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9525741268224334	0.0005527786369235996	0.9841444919059494	61
HLA-C07:02	QN...M...	9837.7	7.5	CKSFSICLL	2315.8	1.6	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.8807970779778823	1.1399918530430558e-12	0.9841444919059494	56
HLA-A31:01	T.F..R...	14.2	0.09	IVCHKMYLK	131.1	1.0	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.9933071490757153	0.9999288038061921	0.9841444919059494	56
HLA-A31:01	....E....	506.9	2.5	TILDKLVQR	68.3	0.6	ENSG00000156096	ENST00000305107	E/K	0.563	1	5	4	69495729	45	M	UGT2B4	No	2.44878178	0.9990889488055994	0.07585818002124355	0.9878510119201874	53
HLA-A02:01	E........	9137.4	13.0	KLVQRGHEV	162.5	1.4	ENSG00000156096	ENST00000305107	E/K	0.563	1	1	4	69495729	45	M	UGT2B4	No	2.44878178	0.9525741268224334	1.299581425007503e-24	0.9878510119201874	53
HLA-C07:02	.....G.VY	8919.0	6.5	VIVCHKMYL	2701.8	1.9	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.6224593312018547	1.6918979223288784e-10	0.9841444919059494	40
HLA-C07:02	S..Y...L.	3438.9	2.5	NFEDLFSVI	2684.2	1.9	ENSG00000048028	ENST00000003302	FQ/X	0.650	3	1:9	11	113834326-113834329	181	F	USP28	No	2.31471308	0.6224593312018547	0.07585818002124355	0.9841444919059494	39
HLA-B07:02	...R.....	31.9	0.12	KPGCKTNQL	43.2	0.17	ENSG00000169925	ENST00000371834	R/C	0.333	1	4	9	134053378	34	M	BRD3	Yes	1.86032922	0.9998937914787018	0.9999172827771484	0.9611149444887752	32
HLA-C07:02	R........	1301.2	0.9	CKTNQLQYM	2021.9	1.4	ENSG00000169925	ENST00000371834	R/C	0.333	1	1	9	

.log file

        # VERSION:  MuPeXI 1.1
        # CALL:     /usr/cbs/bio/src/MuPeXI-1.1/mupexi/MuPeXI.py -c /usr/cbs/bio/src/MuPeXI-1.1/config.ini -w -m -v /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.0 -e /usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7/file.1 -a HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03 -l 9
        # DATE:     Monday 15 of August 2016
        # TIME:     15:34:35
        # PWD:      /net/athena/usr/opt/www/webface/tmp/server/mupexi/57B1C4C90000785934C25FC7

        ----------------------------------------------------------------------------------------------------------
                                                        MuPeX
        ----------------------------------------------------------------------------------------------------------

          Reading protein reference file:            Found 99436 sequences, with 0 [9]mers
                                                           of which 0 were unique peptides
          Reading VEP file:                          Found 22 irrelevant mutation consequences which were discarded
                                                     Found 29 missense variant mutation(s) 
                                                           0 insertion(s)
                                                           0 deletion(s)
                                                           3 frameshift variant mutation(s)
                                                     In 7 genes and 32 transcripts
          Checking peptides:                         0 peptides matched a normal peptide and were discarded
                                                     0 peptides included unsupported symbols (e.g. *, X, U) and were discarded 

          Final Result:                              390 potential mutant peptides
          MuPeX Runtime:                             0:00:15.476422

        ----------------------------------------------------------------------------------------------------------
                                                        MuPeI
        ----------------------------------------------------------------------------------------------------------

          Reading through MuPex file:                Found 390 peptides of which 105 were unique
          Detecting HLA alleles:                     Detected the following 6 HLA alleles:
                                                        HLA-A31:01,HLA-A02:01,HLA-B07:02,HLA-B55:01,HLA-C07:02,HLA-C03:03
                                                        of which 6 were unique
          Running NetMHCpan 2.8:                     Analyzed 6 HLA allele(s)
                                                     NetMHCpan runtime: 0:00:05.053376

          MuPeI Runtime:                             0:00:09.374437

          TOTAL Runtime:                             0:00:31.901699

.fasta file

>DTU|ENST00000436792_184838714|M_D9Y
SAQIVSAAYKVDAGLPT
>DTU|ENST00000422105_184838714|M_D9Y
SAQIVSAAYKVDAGLPT
>DTU|ENST00000452666_184838714|M_D9Y
SAQIVSAAYKVDAGLPT
>DTU|ENST00000380779_10567210|M_S9F
AFDANTMTFAEKVLCQF
>DTU|ENST00000424463_184838714|M_D9Y
SAQIVSAAYKVDAGLPT
>DTU|ENST00000510114_69495729|M_E9K
MNIKTILDKLVQRGHEV
>DTU|ENST00000610939_10567210|M_S9F
AFDANTMTFAEKVLCQF
>DTU|ENST00000446204_184838714|M_D9Y
SAQIVSAAYKVDAGLPT
>DTU|ENST00000512583_69495729|M_E9K
MNIKTILDKLVQRGHEV
>DTU|ENST00000305107_69495729|M_E9K
MNIKTILDKLVQRGHEV
>DTU|ENST00000317552_10567210|M_S9F
AFDANTMTFAEKVLCQF
>DTU|ENST00000545540_113834326-113834329|F_FQ9:51X
FSAVIQSLNNCLNFEDLFSVIVCHKMYLKIVEVIQKREISCLCKSFSICLL
>DTU|ENST00000426319_184838714|M_D9Y
TFSEFNPYYKVDAGLPT



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