diff --git a/wilson-basic/data/B_Methylation_Hautefort_Oncot_2017.se b/wilson-basic/data/B_Methylation_Hautefort_Oncot_2017.se index 76cf9cf..e5d7ca1 100644 --- a/wilson-basic/data/B_Methylation_Hautefort_Oncot_2017.se +++ b/wilson-basic/data/B_Methylation_Hautefort_Oncot_2017.se @@ -1,21 +1,21 @@ !format=SummarizedExperiment !version=1.0 !experiment_id=123456 -#key factor1 level type label sub_label -#Feature gene id feature unique_id unique id -#Gene feature category Gene name -#GeneID feature category Ensembl ID -#Type feature category feature type -#Chr feature category Chr -#Start feature category start -#Stop feature category stop -#Strand feature category strand -#P-val control contrast probability control P-val -#Q-val control contrast probability control Q-val -#P-val all contrast probability all_PAH P-val -#Q-val all contrast probability all_PAH Q-val -#Higher in feature category higher_in -#with Q-val contrast probability direction Q-val +#key level type label sub_label +#Feature feature unique_id unique id +#Gene feature category Gene name +#GeneID feature category Ensembl ID +#Type feature category feature type +#Chr feature category Chr +#Start feature category start +#Stop feature category stop +#Strand feature category strand +#P-val control contrast probability control P-val +#Q-val control contrast probability control Q-val +#P-val all contrast probability all_PAH P-val +#Q-val all contrast probability all_PAH Q-val +#Higher in feature category higher_in +#with Q-val contrast probability direction Q-val Feature Gene GeneID Type Chr Start Stop Strand P-val control Q-val control P-val all Q-val all Higher in with Q-val MXRA8-009-exon-2 MXRA8 ENSG00000162576.12 protein_coding chr1 1289573 1289889 - 1 1 2.81E-06 0.004315 all 0.004315 MXRA8-001-exon-6 MXRA8 ENSG00000162576.12 protein_coding chr1 1289734 1289889 - 1 1 2.81E-06 0.008776 all 0.008776 diff --git a/wilson-basic/data/C_Proteomics_Worzfeld_MCP_2017.se b/wilson-basic/data/C_Proteomics_Worzfeld_MCP_2017.se index 961359b..d21b941 100644 --- a/wilson-basic/data/C_Proteomics_Worzfeld_MCP_2017.se +++ b/wilson-basic/data/C_Proteomics_Worzfeld_MCP_2017.se @@ -2,90 +2,90 @@ !version= !experiment_id= !delimiter=; -#key factor1 level type label sub_label -#Protein IDs feature array IDs proteins -#Majority protein IDs feature array IDs majority protein -#Fasta headers feature array fasta headers -#id feature unique_id unique identifier -#Peptide IDs feature array IDs peptide -#Mod. peptide IDs feature array IDs mod. peptide -#Mol. weight [kDa] feature category Mol. weight [kDa] -#Sequence length feature category length Sequence -#Sequence lengths feature array lengths Sequence -#Reverse feature category Reverse -#Potential contaminant feature category Potential contaminant -#Peptides P105_Ma sample score P105_Ma Peptides -#Peptides P105_Sp sample score P105_Sp Peptides -#Peptides P105_Tc sample score P105_Tc Peptides -#Peptides P108_Ma sample score P108_Ma Peptides -#Peptides P108_Sp sample score P108_Sp Peptides -#Peptides P108_Tc sample score P108_Tc Peptides -#Peptides P114_Ma sample score P114_Ma Peptides -#Peptides P114_Sp sample score P114_Sp Peptides -#Peptides P114_Tc sample score P114_Tc Peptides -#Peptides P117_Ma sample score P117_Ma Peptides -#Peptides P117_Sp sample score P117_Sp Peptides -#Peptides P117_Tc sample score P117_Tc Peptides -#Razor + unique peptides P105_Ma sample score P105_Ma Razor + unique peptides -#Razor + unique peptides P105_Sp sample score P105_Sp Razor + unique peptides -#Razor + unique peptides P105_Tc sample score P105_Tc Razor + unique peptides -#Razor + unique peptides P108_Ma sample score P108_Ma Razor + unique peptides -#Razor + unique peptides P108_Sp sample score P108_Sp Razor + unique peptides -#Razor + unique peptides P108_Tc sample score P108_Tc Razor + unique peptides -#Razor + unique peptides P114_Ma sample score P114_Ma Razor + unique peptides -#Razor + unique peptides P114_Sp sample score P114_Sp Razor + unique peptides -#Razor + unique peptides P114_Tc sample score P114_Tc Razor + unique peptides -#Razor + unique peptides P117_Ma sample score P117_Ma Razor + unique peptides -#Razor + unique peptides P117_Sp sample score P117_Sp Razor + unique peptides -#Razor + unique peptides P117_Tc sample score P117_Tc Razor + unique peptides -#Unique peptides P105_Ma sample score P105_Ma Unique peptides -#Unique peptides P105_Sp sample score P105_Sp Unique peptides -#Unique peptides P105_Tc sample score P105_Tc Unique peptides -#Unique peptides P108_Ma sample score P108_Ma Unique peptides -#Unique peptides P108_Sp sample score P108_Sp Unique peptides -#Unique peptides P108_Tc sample score P108_Tc Unique peptides -#Unique peptides P114_Ma sample score P114_Ma Unique peptides -#Unique peptides P114_Sp sample score P114_Sp Unique peptides -#Unique peptides P114_Tc sample score P114_Tc Unique peptides -#Unique peptides P117_Ma sample score P117_Ma Unique peptides -#Unique peptides P117_Sp sample score P117_Sp Unique peptides -#Unique peptides P117_Tc sample score P117_Tc Unique peptides -#Sequence coverage P105_Ma [%] sample ratio P105_Ma Sequence coverage [%] -#Sequence coverage P105_Sp [%] sample ratio P105_Sp Sequence coverage [%] -#Sequence coverage P105_Tc [%] sample ratio P105_Tc Sequence coverage [%] -#Sequence coverage P108_Ma [%] sample ratio P108_Ma Sequence coverage [%] -#Sequence coverage P108_Sp [%] sample ratio P108_Sp Sequence coverage [%] -#Sequence coverage P108_Tc [%] sample ratio P108_Tc Sequence coverage [%] -#Sequence coverage P114_Ma [%] sample ratio P114_Ma Sequence coverage [%] -#Sequence coverage P114_Sp [%] sample ratio P114_Sp Sequence coverage [%] -#Sequence coverage P114_Tc [%] sample ratio P114_Tc Sequence coverage [%] -#Sequence coverage P117_Ma [%] sample ratio P117_Ma Sequence coverage [%] -#Sequence coverage P117_Sp [%] sample ratio P117_Sp Sequence coverage [%] -#Sequence coverage P117_Tc [%] sample ratio P117_Tc Sequence coverage [%] -#Intensity P105_Ma sample score P105_Ma Intensity -#Intensity P105_Sp sample score P105_Sp Intensity -#Intensity P105_Tc sample score P105_Tc Intensity -#Intensity P108_Ma sample score P108_Ma Intensity -#Intensity P108_Sp sample score P108_Sp Intensity -#Intensity P108_Tc sample score P108_Tc Intensity -#Intensity P114_Ma sample score P114_Ma Intensity -#Intensity P114_Sp sample score P114_Sp Intensity -#Intensity P114_Tc sample score P114_Tc Intensity -#Intensity P117_Ma sample score P117_Ma Intensity -#Intensity P117_Sp sample score P117_Sp Intensity -#Intensity P117_Tc sample score P117_Tc Intensity -#LFQ intensity P105_Ma sample score P105_Ma LFQ intensity -#LFQ intensity P105_Sp sample score P105_Sp LFQ intensity -#LFQ intensity P105_Tc sample score P105_Tc LFQ intensity -#LFQ intensity P108_Ma sample score P108_Ma LFQ intensity -#LFQ intensity P108_Sp sample score P108_Sp LFQ intensity -#LFQ intensity P108_Tc sample score P108_Tc LFQ intensity -#LFQ intensity P114_Ma sample score P114_Ma LFQ intensity -#LFQ intensity P114_Sp sample score P114_Sp LFQ intensity -#LFQ intensity P114_Tc sample score P114_Tc LFQ intensity -#LFQ intensity P117_Ma sample score P117_Ma LFQ intensity -#LFQ intensity P117_Sp sample score P117_Sp LFQ intensity -#LFQ intensity P117_Tc sample score P117_Tc LFQ intensity +#key level type label sub_label +#Protein IDs feature array IDs proteins +#Majority protein IDs feature array IDs majority protein +#Fasta headers feature array fasta headers +#id feature unique_id unique identifier +#Peptide IDs feature array IDs peptide +#Mod. peptide IDs feature array IDs mod. peptide +#Mol. weight [kDa] feature category Mol. weight [kDa] +#Sequence length feature category length Sequence +#Sequence lengths feature array lengths Sequence +#Reverse feature category Reverse +#Potential contaminant feature category Potential contaminant +#Peptides P105_Ma sample score P105_Ma Peptides +#Peptides P105_Sp sample score P105_Sp Peptides +#Peptides P105_Tc sample score P105_Tc Peptides +#Peptides P108_Ma sample score P108_Ma Peptides +#Peptides P108_Sp sample score P108_Sp Peptides +#Peptides P108_Tc sample score P108_Tc Peptides +#Peptides P114_Ma sample score P114_Ma Peptides +#Peptides P114_Sp sample score P114_Sp Peptides +#Peptides P114_Tc sample score P114_Tc Peptides +#Peptides P117_Ma sample score P117_Ma Peptides +#Peptides P117_Sp sample score P117_Sp Peptides +#Peptides P117_Tc sample score P117_Tc Peptides +#Razor + unique peptides P105_Ma sample score P105_Ma Razor + unique peptides +#Razor + unique peptides P105_Sp sample score P105_Sp Razor + unique peptides +#Razor + unique peptides P105_Tc sample score P105_Tc Razor + unique peptides +#Razor + unique peptides P108_Ma sample score P108_Ma Razor + unique peptides +#Razor + unique peptides P108_Sp sample score P108_Sp Razor + unique peptides +#Razor + unique peptides P108_Tc sample score P108_Tc Razor + unique peptides +#Razor + unique peptides P114_Ma sample score P114_Ma Razor + unique peptides +#Razor + unique peptides P114_Sp sample score P114_Sp Razor + unique peptides +#Razor + unique peptides P114_Tc sample score P114_Tc Razor + unique peptides +#Razor + unique peptides P117_Ma sample score P117_Ma Razor + unique peptides +#Razor + unique peptides P117_Sp sample score P117_Sp Razor + unique peptides +#Razor + unique peptides P117_Tc sample score P117_Tc Razor + unique peptides +#Unique peptides P105_Ma sample score P105_Ma Unique peptides +#Unique peptides P105_Sp sample score P105_Sp Unique peptides +#Unique peptides P105_Tc sample score P105_Tc Unique peptides +#Unique peptides P108_Ma sample score P108_Ma Unique peptides +#Unique peptides P108_Sp sample score P108_Sp Unique peptides +#Unique peptides P108_Tc sample score P108_Tc Unique peptides +#Unique peptides P114_Ma sample score P114_Ma Unique peptides +#Unique peptides P114_Sp sample score P114_Sp Unique peptides +#Unique peptides P114_Tc sample score P114_Tc Unique peptides +#Unique peptides P117_Ma sample score P117_Ma Unique peptides +#Unique peptides P117_Sp sample score P117_Sp Unique peptides +#Unique peptides P117_Tc sample score P117_Tc Unique peptides +#Sequence coverage P105_Ma [%] sample ratio P105_Ma Sequence coverage [%] +#Sequence coverage P105_Sp [%] sample ratio P105_Sp Sequence coverage [%] +#Sequence coverage P105_Tc [%] sample ratio P105_Tc Sequence coverage [%] +#Sequence coverage P108_Ma [%] sample ratio P108_Ma Sequence coverage [%] +#Sequence coverage P108_Sp [%] sample ratio P108_Sp Sequence coverage [%] +#Sequence coverage P108_Tc [%] sample ratio P108_Tc Sequence coverage [%] +#Sequence coverage P114_Ma [%] sample ratio P114_Ma Sequence coverage [%] +#Sequence coverage P114_Sp [%] sample ratio P114_Sp Sequence coverage [%] +#Sequence coverage P114_Tc [%] sample ratio P114_Tc Sequence coverage [%] +#Sequence coverage P117_Ma [%] sample ratio P117_Ma Sequence coverage [%] +#Sequence coverage P117_Sp [%] sample ratio P117_Sp Sequence coverage [%] +#Sequence coverage P117_Tc [%] sample ratio P117_Tc Sequence coverage [%] +#Intensity P105_Ma sample score P105_Ma Intensity +#Intensity P105_Sp sample score P105_Sp Intensity +#Intensity P105_Tc sample score P105_Tc Intensity +#Intensity P108_Ma sample score P108_Ma Intensity +#Intensity P108_Sp sample score P108_Sp Intensity +#Intensity P108_Tc sample score P108_Tc Intensity +#Intensity P114_Ma sample score P114_Ma Intensity +#Intensity P114_Sp sample score P114_Sp Intensity +#Intensity P114_Tc sample score P114_Tc Intensity +#Intensity P117_Ma sample score P117_Ma Intensity +#Intensity P117_Sp sample score P117_Sp Intensity +#Intensity P117_Tc sample score P117_Tc Intensity +#LFQ intensity P105_Ma sample score P105_Ma LFQ intensity +#LFQ intensity P105_Sp sample score P105_Sp LFQ intensity +#LFQ intensity P105_Tc sample score P105_Tc LFQ intensity +#LFQ intensity P108_Ma sample score P108_Ma LFQ intensity +#LFQ intensity P108_Sp sample score P108_Sp LFQ intensity +#LFQ intensity P108_Tc sample score P108_Tc LFQ intensity +#LFQ intensity P114_Ma sample score P114_Ma LFQ intensity +#LFQ intensity P114_Sp sample score P114_Sp LFQ intensity +#LFQ intensity P114_Tc sample score P114_Tc LFQ intensity +#LFQ intensity P117_Ma sample score P117_Ma LFQ intensity +#LFQ intensity P117_Sp sample score P117_Sp LFQ intensity +#LFQ intensity P117_Tc sample score P117_Tc LFQ intensity Protein IDs Majority protein IDs Fasta headers id Peptide IDs Mod. peptide IDs Mol. weight [kDa] Sequence length Sequence lengths Reverse Potential contaminant Peptides P105_Ma Peptides P105_Sp Peptides P105_Tc Peptides P108_Ma Peptides P108_Sp Peptides P108_Tc Peptides P114_Ma Peptides P114_Sp Peptides P114_Tc Peptides P117_Ma Peptides P117_Sp Peptides P117_Tc Razor + unique peptides P105_Ma Razor + unique peptides P105_Sp Razor + unique peptides P105_Tc Razor + unique peptides P108_Ma Razor + unique peptides P108_Sp Razor + unique peptides P108_Tc Razor + unique peptides P114_Ma Razor + unique peptides P114_Sp Razor + unique peptides P114_Tc Razor + unique peptides P117_Ma Razor + unique peptides P117_Sp Razor + unique peptides P117_Tc Unique peptides P105_Ma Unique peptides P105_Sp Unique peptides P105_Tc Unique peptides P108_Ma Unique peptides P108_Sp Unique peptides P108_Tc Unique peptides P114_Ma Unique peptides P114_Sp Unique peptides P114_Tc Unique peptides P117_Ma Unique peptides P117_Sp Unique peptides P117_Tc Sequence coverage P105_Ma [%] Sequence coverage P105_Sp [%] Sequence coverage P105_Tc [%] Sequence coverage P108_Ma [%] Sequence coverage P108_Sp [%] Sequence coverage P108_Tc [%] Sequence coverage P114_Ma [%] Sequence coverage P114_Sp [%] Sequence coverage P114_Tc [%] Sequence coverage P117_Ma [%] Sequence coverage P117_Sp [%] Sequence coverage P117_Tc [%] Intensity P105_Ma Intensity P105_Sp Intensity P105_Tc Intensity P108_Ma Intensity P108_Sp Intensity P108_Tc Intensity P114_Ma Intensity P114_Sp Intensity P114_Tc Intensity P117_Ma Intensity P117_Sp Intensity P117_Tc LFQ intensity P105_Ma LFQ intensity P105_Sp LFQ intensity P105_Tc LFQ intensity P108_Ma LFQ intensity P108_Sp LFQ intensity P108_Tc LFQ intensity P114_Ma LFQ intensity P114_Sp LFQ intensity P114_Tc LFQ intensity P117_Ma LFQ intensity P117_Sp LFQ intensity P117_Tc CON__A2A4G1 CON__A2A4G1 0 22949;28099;42521;51223;76404;86903;86904;88376;88379;91428;116372;136504;136786;153079;153238;157120;159513;168844;174763;174764;175705 25794;31656;47837;47838;57578;85772;97394;97395;99047;99050;102408;133096;155401;155402;155713;173959;173960;174139;178503;178504;181277;191750;198526;198527;198528;198529;199576 49.493 456 456 + 12 15 11 13 14 13 14 15 11 11 12 12 2 1 0 2 2 1 1 0 0 0 0 0 2 1 0 2 2 1 1 0 0 0 0 0 26.8 21.3 15.4 28.1 22.8 19.1 28.1 21.3 16.7 14 14.3 15.6 42445000 40975000 0 28410000 44256000 15290000 2044500 0 0 0 0 0 16418000 0 0 54775000 0 0 0 0 0 0 0 0 CON__A2A5Y0;ENSP00000458693;ENSP00000225550;CON__O76014 CON__A2A5Y0 1 16862;42134;73147;86903;86906;90329;100590;108242;116378;129509;138732;155258;156026;179828 19040;47402;47403;81978;97394;97397;101188;112783;121164;133105;147821;157841;176397;177268;204150 47.117 416 416;449;449;471 + 2 2 6 2 2 3 5 10 1 4 7 6 0 0 1 0 0 0 0 4 0 0 0 1 0 0 1 0 0 0 0 3 0 0 0 1 4.3 3.8 13.9 4.3 4.3 7.5 10.3 19 1.7 8.4 15.1 14.2 0 0 5617900 0 0 0 0 473340000 0 0 0 2282600 0 0 0 0 0 0 0 423120000 0 0 0 0