diff --git a/cancermuts/datasources.py b/cancermuts/datasources.py index 53a34f3e..b4b0d386 100644 --- a/cancermuts/datasources.py +++ b/cancermuts/datasources.py @@ -1846,12 +1846,12 @@ def __init__(self, database_dir, database_files=None): self._ptm_types = ['acetylation', 'methylation', 'O-GalNAc', 'O-GlcNAc', 'phosphorylation', 'sumoylation', 'ubiquitination'] self._ptm_types_to_classes = { 'acetylation' : 'ptm_acetylation', 'methylation' : 'ptm_methylation', - 'O-GalNAc' : 'ptm_ogalnac', - 'O-GlcNAc' : 'ptm_oglcnac', + 'O-GalNAc' : 'ptm_glycosylation', + 'O-GlcNAc' : 'ptm_glycosylation', 'phosphorylation' : 'ptm_phosphorylation', 'sumoylation' : 'ptm_sumoylation', 'ubiquitination' : 'ptm_ubiquitination' } - self._ptm_suffixes = ['ac', 'm[0-9]', 'ga', 'gl', 'p', 'sm', 'ub'] + self._ptm_suffixes = ['ac', 'm[0-9]', 'gly', 'gly', 'p', 'sm', 'ub'] self._ptm_suffix_offsets = [-3, -3, -3, -3, -2, -3, -3] self._database_dir = database_dir @@ -1931,6 +1931,30 @@ def add_position_properties(self, sequence, properties=None): ) position.add_property(property_obj) self.log.info("adding %s to site %s" % (m, property_obj.name)) + + is_gly = False + has_gly_site = False + has_gly_sub = False + for prop in position.properties.values(): + if prop.category == 'ptm_glycosylation': + is_gly = True + break + + has_gly_site = any(prop.category == 'ptm_glycosylation' for prop in position.properties.values()) + if not has_gly_site: + gly_site = position_properties_classes['ptm_glycosylation']( + position=position, + sources=[self]) + position.add_property(gly_site) + + has_gly_subtype = any(prop.header == 'glycosylation_subtype' for prop in position.properties.values()) + if not has_gly_subtype: + gly_sub = position_properties_classes['glycosylation_subtype']( + position=position, + sources=[self], + subtype="" + ) + position.add_property(gly_sub) class MyVariant(DynamicSource, object): @logger_init diff --git a/cancermuts/properties.py b/cancermuts/properties.py index 48050ee6..c3a92414 100644 --- a/cancermuts/properties.py +++ b/cancermuts/properties.py @@ -173,15 +173,15 @@ def __init__(self, position, sources): def get_value_str(self): return self.code - -class OGalNAcSite(PositionProperty): - description = "OGalNAc site" - header = "ogalnac_site" - category='ptm_ogalnac' - code = "O-GalNAc" + +class GlycosylationSite(PositionProperty): + description = "Glycosylation site" + header = "glycosylation_site" + category='ptm_glycosylation' + code = "Gly" def __init__(self, position, sources): - super(OGalNAcSite, self).__init__( name="o-GalNAc Site", + super(GlycosylationSite, self).__init__( name="Glycosylation Site", position=position, sources=sources, values={}, @@ -189,31 +189,37 @@ def __init__(self, position, sources): def get_value_str(self): return self.code + +class GlycosylationSubtype(PositionProperty): + description = "Glycosylation Subtype" + header = "glycosylation_subtype" + category="glycosylation_subtype" + #code = -class OGlcNAcSite(PositionProperty): - description = "OGlcNAc site" - header = "oglcnac_site" - category='ptm_oglcnac' - code = "O-GlcNAc" - + subtype = "" - def __init__(self, position, sources): - super(OGlcNAcSite, self).__init__( name="o-GlcNAc Site", + def __init__(self, position, sources, subtype): + super(GlycosylationSubtype, self).__init__( name="GlycosylationSubtype", position=position, sources=sources, - values={}, + values={"subtype": subtype}, metadata={} ) def get_value_str(self): - return self.code - + return self.values.get("subtype", "") + #return self.values.get("subtype") + #val = self.values.get("subtype") + #if val is None: + #return "" + #else: + #return str(val) + class SumoylationSite(PositionProperty): description = "Sumoylation site" header = "sumoyylation_site" category='ptm_sumoylation' code = "Sumo" - def __init__(self, position, sources): super(SumoylationSite, self).__init__( name="Sumoylation Site", position=position, @@ -306,8 +312,8 @@ def __init__(self, position, sources): 'ptm_methylation' : MethylationSite, 'ptm_acetylation' : AcetylationSite, 'ptm_nitrosylation' : SNitrosylationSite, - 'ptm_ogalnac' : OGalNAcSite, - 'ptm_oglcnac' : OGlcNAcSite, + 'ptm_glycosylation' : GlycosylationSite, + 'glycosylation_subtype' : GlycosylationSubtype, 'ptm_sumoylation' : SumoylationSite, 'ptm_ubiquitination' : UbiquitinationSite, 'ptm_cleavage' : CleavageSite, diff --git a/cancermuts/table.py b/cancermuts/table.py index 0d0e2c13..7a19a559 100644 --- a/cancermuts/table.py +++ b/cancermuts/table.py @@ -125,8 +125,8 @@ class Table: ptm_colors = defaultdict(lambda: 'black', { 'ptm_acetylation' : 'grey', 'ptm_methylation' : 'darkgreen', - 'ptm_ogalnac' : 'orange', - 'ptm_oglcnac' : 'darkorange', + 'ptm_glycosylation' : 'orange', + 'ptm_gly_subtype' : 'darkorange', 'ptm_phosphorylation' : 'red', 'ptm_ubiquitination' : 'blue', 'ptm_sumoylation' : 'lightblue', @@ -181,7 +181,7 @@ def __init__(self, labels=None, ptm_colors=None, y_ptm=1.02): def to_dataframe(self, sequence, mutation_metadata=["cancer_study", "cancer_type", "genomic_coordinates", "genomic_mutations", "revel_score", "cancer_site", "cancer_histology",'gnomad_exome_allele_frequency', 'gnomad_genome_allele_frequency', 'gnomad_popmax_exome_allele_frequency', 'gnomad_popmax_genome_allele_frequency', 'clinvar_variant_id', 'clinvar_germline_classification', 'clinvar_germline_condition', 'clinvar_germline_review_status', 'clinvar_oncogenicity_classification', 'clinvar_oncogenicity_condition', 'clinvar_oncogenicity_review_status', 'clinvar_clinical_impact_classification', 'clinvar_clinical_impact_condition', 'clinvar_clinical_impact_review_status'], - position_properties=['ptm_phosphorylation','ptm_methylation','ptm_ubiquitination','ptm_cleavage', 'ptm_nitrosylation','ptm_acetylation', 'ptm_sumoylation', 'ptm_ogalnac', 'ptm_oglcnac', 'mobidb_disorder_propensity'], + position_properties=['ptm_phosphorylation','ptm_methylation','ptm_ubiquitination','ptm_cleavage', 'ptm_nitrosylation','ptm_acetylation', 'ptm_sumoylation', 'ptm_glycosylation', 'glycosylation_subtype', 'mobidb_disorder_propensity'], sequence_properties=['linear_motif', 'structure']): rows = [] diff --git a/docs/metatable.csv b/docs/metatable.csv index 1ba4d68e..2d967db3 100644 --- a/docs/metatable.csv +++ b/docs/metatable.csv @@ -1,16 +1,16 @@ -,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,ogalnac_site,oglcnac_site,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status +,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,glycosylation_site,glycosylation_subtype,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status 0,1,M,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 1,2,P,R,,,,,,,,,,,,,,ClinVar,,,"hg19,16:87426038-87426038, hg38,16:87392432-87392432","hg19,16:g.87426038C>G, hg38,16:g.87392432C>G",0.145,,,0.0000000000000000,,,,2358122,Uncertain significance,not specified,1,,,,,, 2,3,S,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 3,4,E,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -4,5,K,,,,Ubq,,,,,,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, -5,6,T,,P,,,,,,,,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, +4,5,K,,,,Ubq,,,,,Gly,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, +5,6,T,,P,,,,,,,Gly,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 6,7,F,,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 7,8,K,,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 8,9,Q,,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 9,10,R,,,,,,,,,,,,,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 10,11,R,L,,,,,,,,,,,,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,ClinVar,,,"hg19,16:87426065-87426065, hg38,16:87392459-87392459","hg19,16:g.87426065G>T, hg38,16:g.87392459G>T",0.226,,,0.0000000000000000,,,,2226367,Uncertain significance,not specified,1,,,,,, -11,12,T,,P,,,,,,,,,,PhosphoSite,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, +11,12,T,,P,,,,,,,Gly,,,PhosphoSite,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 12,13,F,,,,,,,,,,,,,"14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 13,14,E,,,,,,,,,,,,,"14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 14,15,Q,R,,,,,,,,,,,,,,ClinVar,,,"hg19,16:87432424-87432424, hg38,16:87398818-87398818","hg19,16:g.87432424A>G, hg38,16:g.87398818A>G",0.193,,,0.0000079532982328,,,,3542641,Uncertain significance,not specified,1,,,,,, @@ -19,7 +19,7 @@ 17,18,E,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 18,19,D,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 19,20,V,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, -20,21,R,,,Me,,,,,,,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, +20,21,R,,,Me,,,,,,Gly,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 21,22,L,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 22,23,I,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 23,24,R,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@ -27,9 +27,9 @@ 25,26,Q,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 26,27,H,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 27,28,P,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -28,29,T,I,P,,,,,,,,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>T, hg38,16:g.87398860C>T",0.168,,,0.0000079527922254,,,,2493543,Uncertain significance,not specified,1,,,,,, -29,29,T,N,P,,,,,,,,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>A, hg38,16:g.87398860C>A",0.067,,,0.0000278347727887,0.0000636739891754,,,4051121,Uncertain significance,not specified,1,,,,,, -30,30,K,,,,Ubq,,,,,,,,PhosphoSite,,,,,,,,,,,,,,,,,,,,,,,, +28,29,T,I,P,,,,,,,Gly,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>T, hg38,16:g.87398860C>T",0.168,,,0.0000079527922254,,,,2493543,Uncertain significance,not specified,1,,,,,, +29,29,T,N,P,,,,,,,Gly,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>A, hg38,16:g.87398860C>A",0.067,,,0.0000278347727887,0.0000636739891754,,,4051121,Uncertain significance,not specified,1,,,,,, +30,30,K,,,,Ubq,,,,,Gly,,,PhosphoSite,,,,,,,,,,,,,,,,,,,,,,,, 31,31,I,,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,,,,,,,,,,,,,,,,,,,,,, 32,32,P,,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,,,,,,,,,,,,,,,,,,,,,, 33,33,V,,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,,,,,,,,,,,,,,,,,,,,,, @@ -41,7 +41,7 @@ 39,39,K,R,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,cBioPortal,coadread_tcga_pan_can_atlas_2018,Colorectal Adenocarcinoma,"hg19,16:87435800-87435800","hg19,16:g.87435800A>G",0.065,,,,,,,,,,,,,,,, 40,40,G,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 41,41,E,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, -42,42,K,,,,Ubq,,,,,,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, +42,42,K,,,,Ubq,,,,,Gly,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 43,43,Q,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 44,44,L,F,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,ClinVar,,,"hg19,16:87435814-87435814, hg38,16:87402208-87402208","hg19,16:g.87435814C>T, hg38,16:g.87402208C>T",0.359,,,,,,,2298840,Uncertain significance,not specified,1,,,,,, 45,44,L,P,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,ClinVar,,,"hg19,16:87435815-87435815, hg38,16:87402209-87402209","hg19,16:g.87435815T>C, hg38,16:g.87402209T>C",0.632,,,,,,,2298841,Uncertain significance,not specified,1,,,,,, @@ -49,9 +49,9 @@ 47,46,V,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 48,47,L,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 49,48,D,,,,,,,,,,,,,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, -50,49,K,,,,Ubq,,,Ac,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, -51,50,T,R,P,,,,,,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,ClinVar,,,"hg19,16:87435833-87435833, hg38,16:87402227-87402227","hg19,16:g.87435833C>G, hg38,16:g.87402227C>G",0.415,,,0.0000039767440011,,,,3870023,Uncertain significance,not specified,1,,,,,, -52,51,K,,,,Ubq,,,Ac,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, +50,49,K,,,,Ubq,,,Ac,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, +51,50,T,R,P,,,,,,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,ClinVar,,,"hg19,16:87435833-87435833, hg38,16:87402227-87402227","hg19,16:g.87435833C>G, hg38,16:g.87402227C>G",0.415,,,0.0000039767440011,,,,3870023,Uncertain significance,not specified,1,,,,,, +52,51,K,,,,Ubq,,,Ac,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 53,52,F,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 54,53,L,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 55,54,V,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|Arc N-lobe binding ligand (LIG_Arc_Nlobe_1), 54-58, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, @@ -65,7 +65,7 @@ 63,62,E,,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 64,63,L,,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 65,64,I,,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, -66,65,K,E,,,Ubq,,,,,,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,"cBioPortal,COSMIC",coadread_genentech,Colorectal Adenocarcinoma,"hg19,16:87435877-87435877, hg38,16:87402271-87402271","hg19,16:g.87435877A>G, hg38,16:g.87402271A>G",0.314,"large_intestine, colon","carcinoma, adenocarcinoma",0.0000278640235650,,,,,,,,,,,,, +66,65,K,E,,,Ubq,,,,,Gly,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,"cBioPortal,COSMIC",coadread_genentech,Colorectal Adenocarcinoma,"hg19,16:87435877-87435877, hg38,16:87402271-87402271","hg19,16:g.87435877A>G, hg38,16:g.87402271A>G",0.314,"large_intestine, colon","carcinoma, adenocarcinoma",0.0000278640235650,,,,,,,,,,,,, 67,66,I,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 68,67,I,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 67-70, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 69,68,R,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 67-70, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 68-70, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, diff --git a/docs/metatable_non_canonical.csv b/docs/metatable_non_canonical.csv index 814aaeee..58f83ce8 100644 --- a/docs/metatable_non_canonical.csv +++ b/docs/metatable_non_canonical.csv @@ -1,4 +1,4 @@ -,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,ogalnac_site,oglcnac_site,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status +,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,glycosylation_site,glycosylation_subtype,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status 0,1,M,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 1,2,K,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 2,3,V,D,,,,,,,,,,,,,,COSMIC,,,"hg38,11:46548373-46548373","hg38,11:g.46548373A>T",0.373,large_intestine,"carcinoma, adenocarcinoma",,,,,,,,,,,,,, diff --git a/docs/metatable_pancancer.csv b/docs/metatable_pancancer.csv index 0a2cbcf5..930fe5c9 100644 --- a/docs/metatable_pancancer.csv +++ b/docs/metatable_pancancer.csv @@ -1,18 +1,18 @@ -,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,ogalnac_site,oglcnac_site,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status +,aa_position,ref_aa,alt_aa,phosphorylation_site,methylation_site,ubiquitination_site,cleavage_site,s-nitrosylation_site,acetylation_site,sumoyylation_site,glycosylation_site,glycosylation_subtype,disorder_propensity,ptm_sources,linear_motif,structure,sources,cancer_study,cancer_type,genomic_coordinates,genomic_mutation,REVEL_score,cancer_site,cancer_histology,gnomad_exome_af,gnomad_genome_af,gnomad_popmax_exome_af,gnomad_popmax_genome_af,clinvar_variant_id,clinvar_germline_classification,clinvar_germline_condition,clinvar_germline_review_status,clinvar_oncogenicity_classification,clinvar_oncogenicity_condition,clinvar_oncogenicity_review_status,clinvar_clinical_impact_classification,clinvar_clinical_impact_condition,clinvar_clinical_impact_review_status 0,1,M,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 1,2,P,R,,,,,,,,,,,,,,ClinVar,,,"hg19,16:87426038-87426038, hg38,16:87392432-87392432","hg19,16:g.87426038C>G, hg38,16:g.87392432C>G",0.145,,,0.0000000000000000,,,,2358122,Uncertain significance,not specified,1,,,,,, 2,2,P,S,,,,,,,,,,,,,,cBioPortal,"ccle_broad_2019, ccle_broad_2025, ccle_genentech_2014",Mixed Cancer Types,"hg19,16:87392431-87392431, hg19,16:87426037-87426037","hg19,16:g.87392431C>T, hg19,16:g.87426037C>T",0.055,,,0.0000405975966223,,,,,,,,,,,,, 3,3,S,L,,,,,,,,,,,,,,COSMIC,,,"hg38,16:87392435-87392435","hg38,16:g.87392435C>T",0.227,"eye, urinary_tract, bladder","carcinoma, small_cell_carcinoma, retinoblastoma",0.0012579161967554,,,,,,,,,,,,, 4,3,S,W,,,,,,,,,,,,,,COSMIC,,,"hg38,16:87392435-87392435","hg38,16:g.87392435C>G",0.158,oesophagus,"carcinoma, squamous_cell_carcinoma",0.0000216882102889,0.0000321957501610,,,,,,,,,,,, 5,4,E,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -6,5,K,,,,Ubq,,,,,,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, -7,6,T,,P,,,,,,,,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, +6,5,K,,,,Ubq,,,,,Gly,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, +7,6,T,,P,,,,,,,Gly,,,PhosphoSite,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 8,7,F,,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,,,,,,,,,,,,,,,,,,,,,, 9,8,K,N,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,COSMIC,,,"hg38,16:87392451-87392451","hg38,16:g.87392451G>T",0.159,"skin, back","adnexal_tumour, malignant_adnexal_tumour, spiradenocarcinoma",0.0000000000000000,,,,,,,,,,,,, 10,9,Q,H,,,,,,,,,,,,"PCSK cleavage site (CLV_PCSK_SKI1_1), 5-9, ELM",,cBioPortal,pancan_pdmr_2025,Mixed Cancer Types,"hg19,16:87426060-87426060","hg19,16:g.87426060G>C",0.156,,,,,,,,,,,,,,,, 11,10,R,,,,,,,,,,,,,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 12,11,R,L,,,,,,,,,,,,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,"cBioPortal,ClinVar",lusc_cptac_2021,Lung Squamous Cell Carcinoma,"hg19,16:87426065-87426065, hg38,16:87392459-87392459","hg19,16:g.87426065G>T, hg38,16:g.87392459G>T",0.226,,,0.0000000000000000,,,,2226367,Uncertain significance,not specified,1,,,,,, -13,12,T,S,P,,,,,,,,,,PhosphoSite,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,COSMIC,,,"hg38,16:87392461-87392461","hg38,16:g.87392461A>T",0.097,"haematopoietic_and_lymphoid_tissue, abdomen","lymphoid_neoplasm, Burkitt_lymphoma, endemic_variant",,,,,,,,,,,,,, +13,12,T,S,P,,,,,,,Gly,,,PhosphoSite,"NRD cleavage site (CLV_NRD_NRD_1), 10-12, ELM|14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,COSMIC,,,"hg38,16:87392461-87392461","hg38,16:g.87392461A>T",0.097,"haematopoietic_and_lymphoid_tissue, abdomen","lymphoid_neoplasm, Burkitt_lymphoma, endemic_variant",,,,,,,,,,,,,, 14,13,F,,,,,,,,,,,,,"14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 15,14,E,,,,,,,,,,,,,"14-3-3 binding phosphopeptide motif (LIG_14-3-3_CanoR_1), 10-14, ELM",,,,,,,,,,,,,,,,,,,,,,, 16,15,Q,R,,,,,,,,,,,,,,ClinVar,,,"hg19,16:87432424-87432424, hg38,16:87398818-87398818","hg19,16:g.87432424A>G, hg38,16:g.87398818A>G",0.193,,,0.0000079532982328,,,,3542641,Uncertain significance,not specified,1,,,,,, @@ -21,8 +21,8 @@ 19,18,E,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 20,19,D,Y,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,cBioPortal,mixed_pipseq_2017,Mixed Cancer Types,"hg19,16:87432435-87432435","hg19,16:g.87432435G>T",0.524,,,,,,,,,,,,,,,, 21,20,V,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, -22,21,R,G,,Me,,,,,,,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,cBioPortal,skcm_tcga,Cutaneous Melanoma,"hg19,16:87432441-87432441","hg19,16:g.87432441C>G",0.125,,,,,,,,,,,,,,,, -23,21,R,Q,,Me,,,,,,,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,"cBioPortal,COSMIC","coad_cptac_2019, pancan_pdmr_2025, ucec_tcga, ucec_tcga_gdc, ucec_tcga_pan_can_atlas_2018, ucec_tcga_pub, ucs_jhu_2014","Colon Adenocarcinoma, Endometrial Carcinoma, Mixed Cancer Types, Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","hg19,16:87398836-87398836, hg19,16:87432442-87432442, hg38,16:87398836-87398836","hg19,16:g.87398836G>A, hg19,16:g.87432442G>A, hg38,16:g.87398836G>A",0.066,endometrium,"carcinoma, endometrioid_carcinoma",0.0000079526657336,,,,,,,,,,,,, +22,21,R,G,,Me,,,,,,Gly,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,cBioPortal,skcm_tcga,Cutaneous Melanoma,"hg19,16:87432441-87432441","hg19,16:g.87432441C>G",0.125,,,,,,,,,,,,,,,, +23,21,R,Q,,Me,,,,,,Gly,,,PhosphoSite,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,"cBioPortal,COSMIC","coad_cptac_2019, pancan_pdmr_2025, ucec_tcga, ucec_tcga_gdc, ucec_tcga_pan_can_atlas_2018, ucec_tcga_pub, ucs_jhu_2014","Colon Adenocarcinoma, Endometrial Carcinoma, Mixed Cancer Types, Uterine Carcinosarcoma/Uterine Malignant Mixed Mullerian Tumor","hg19,16:87398836-87398836, hg19,16:87432442-87432442, hg38,16:87398836-87398836","hg19,16:g.87398836G>A, hg19,16:g.87432442G>A, hg38,16:g.87398836G>A",0.066,endometrium,"carcinoma, endometrioid_carcinoma",0.0000079526657336,,,,,,,,,,,,, 24,22,L,,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,,,,,,,,,,,,,,,,,,,,,, 25,23,I,F,,,,,,,,,,,,"Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_BaEn_1), 18-23, ELM|Adaptin binding Endosome-Lysosome-Basolateral sorting signals (TRG_DiLeu_LyEn_5), 18-23, ELM",,"cBioPortal,COSMIC",nsclc_mskcc_2018,Non-Small Cell Lung Cancer,"hg19,16:87432447-87432447, hg38,16:87398841-87398841","hg19,16:g.87432447A>T, hg38,16:g.87398841A>T",0.632,lung,"carcinoma, squamous_cell_carcinoma",,,,,,,,,,,,,, 26,24,R,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, @@ -30,10 +30,10 @@ 28,26,Q,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 29,27,H,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, 30,28,P,L,,,,,,,,,,,,,,"cBioPortal,COSMIC","skcm_tcga_gdc, skcm_tcga_pan_can_atlas_2018, skcm_tcga_pub_2015",Cutaneous Melanoma,"hg19,16:87398857-87398857, hg19,16:87432463-87432463, hg38,16:87398857-87398857","hg19,16:g.87398857C>T, hg19,16:g.87432463C>T, hg38,16:g.87398857C>T",0.411,skin,malignant_melanoma,,,,,,,,,,,,,, -31,29,T,A,P,,,,,,,,,,PhosphoSite,,,"cBioPortal,COSMIC",gbc_shanghai_2014,Gallbladder Cancer,"hg19,16:87432465-87432465, hg38,16:87398859-87398859","hg19,16:g.87432465A>G, hg38,16:g.87398859A>G",0.147,"biliary_tract, gallbladder","carcinoma, adenocarcinoma",,0.0000955170657157,,,,,,,,,,,, -32,29,T,I,P,,,,,,,,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>T, hg38,16:g.87398860C>T",0.168,,,0.0000079527922254,,,,2493543,Uncertain significance,not specified,1,,,,,, -33,29,T,N,P,,,,,,,,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>A, hg38,16:g.87398860C>A",0.067,,,0.0000278347727887,0.0000636739891754,,,4051121,Uncertain significance,not specified,1,,,,,, -34,30,K,,,,Ubq,,,,,,,,PhosphoSite,,,,,,,,,,,,,,,,,,,,,,,, +31,29,T,A,P,,,,,,,Gly,,,PhosphoSite,,,"cBioPortal,COSMIC",gbc_shanghai_2014,Gallbladder Cancer,"hg19,16:87432465-87432465, hg38,16:87398859-87398859","hg19,16:g.87432465A>G, hg38,16:g.87398859A>G",0.147,"biliary_tract, gallbladder","carcinoma, adenocarcinoma",,0.0000955170657157,,,,,,,,,,,, +32,29,T,I,P,,,,,,,Gly,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>T, hg38,16:g.87398860C>T",0.168,,,0.0000079527922254,,,,2493543,Uncertain significance,not specified,1,,,,,, +33,29,T,N,P,,,,,,,Gly,,,PhosphoSite,,,ClinVar,,,"hg19,16:87432466-87432466, hg38,16:87398860-87398860","hg19,16:g.87432466C>A, hg38,16:g.87398860C>A",0.067,,,0.0000278347727887,0.0000636739891754,,,4051121,Uncertain significance,not specified,1,,,,,, +34,30,K,,,,Ubq,,,,,Gly,,,PhosphoSite,,,,,,,,,,,,,,,,,,,,,,,, 35,31,I,N,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,cBioPortal,pancan_pdmr_2025,Mixed Cancer Types,"hg19,16:87432472-87432472","hg19,16:g.87432472T>A",0.716,,,,,,,,,,,,,,,, 36,32,P,L,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,"cBioPortal,COSMIC",bcc_unige_2016,Basal Cell Carcinoma,"hg19,16:87432474-87432475, hg38,16:87398868-87398869","hg19,16:g.87432474_87432475delinsTT, hg38,16:g.87398868_87398869delinsTT",,skin,"carcinoma, basal_cell_carcinoma",,,,,,,,,,,,,, 37,32,P,Q,,,,,,,,,,,,"PP2A holoenzyme B56-docking site (DOC_PP2A_B56_1), 31-36, ELM|SUMO interaction site (LIG_SUMO_SIM_par_1), 31-36, ELM",,cBioPortal,lusc_tcga_pub,Lung Squamous Cell Carcinoma,"hg19,16:87432475-87432475","hg19,16:g.87432475C>A",0.755,,,,,,,,,,,,,,,, @@ -47,7 +47,7 @@ 45,39,K,R,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,"cBioPortal,COSMIC","coad_tcga_gdc, coadread_tcga_pan_can_atlas_2018","Colon Adenocarcinoma, Colorectal Adenocarcinoma","hg19,16:87402194-87402194, hg19,16:87435800-87435800, hg38,16:87402194-87402194","hg19,16:g.87402194A>G, hg19,16:g.87435800A>G, hg38,16:g.87402194A>G",0.065,"large_intestine, caecum","carcinoma, adenocarcinoma",,,,,,,,,,,,,, 46,40,G,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 47,41,E,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, -48,42,K,,,,Ubq,,,,,,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, +48,42,K,,,,Ubq,,,,,Gly,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 49,43,Q,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,,,,,,,,,,,,,,,,,,,,,, 50,44,L,F,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,ClinVar,,,"hg19,16:87435814-87435814, hg38,16:87402208-87402208","hg19,16:g.87435814C>T, hg38,16:g.87402208C>T",0.359,,,,,,,2298840,Uncertain significance,not specified,1,,,,,, 51,44,L,P,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,ClinVar,,,"hg19,16:87435815-87435815, hg38,16:87402209-87402209","hg19,16:g.87435815T>C, hg38,16:g.87402209T>C",0.632,,,,,,,2298841,Uncertain significance,not specified,1,,,,,, @@ -55,10 +55,10 @@ 53,46,V,F,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 37-46, ELM",,cBioPortal,hgsoc_tcga_gdc,High-Grade Serous Ovarian Cancer,"hg19,16:87402214-87402214","hg19,16:g.87402214G>T",,,,,,,,,,,,,,,,, 54,47,L,M,,,,,,,,,,,,,,cBioPortal,pancan_pdmr_2025,Mixed Cancer Types,"hg19,16:87435823-87435823","hg19,16:g.87435823C>A",0.340,,,,,,,,,,,,,,,, 55,48,D,Y,,,,,,,,,,,,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,cBioPortal,cscc_ranson_2022,Cutaneous Squamous Cell Carcinoma,"hg19,16:87402220-87402220","hg19,16:g.87402220G>T",,,,,,,,,,,,,,,,, -56,49,K,N,,,Ubq,,,Ac,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,"cBioPortal,COSMIC","mixed_allen_2018, skcm_dfci_2015","Cutaneous Melanoma, Mixed Cancer Types","hg19,16:87435831-87435831, hg38,16:87402225-87402225","hg19,16:g.87435831A>C, hg38,16:g.87402225A>C",0.495,skin,malignant_melanoma,,,,,,,,,,,,,, -57,50,T,I,P,,,,,,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,COSMIC,,,"hg38,16:87402227-87402227","hg38,16:g.87402227C>T",0.502,"upper_aerodigestive_tract, mouth, gingiva","carcinoma, squamous_cell_carcinoma",,,,,,,,,,,,,, -58,50,T,R,P,,,,,,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,ClinVar,,,"hg19,16:87435833-87435833, hg38,16:87402227-87402227","hg19,16:g.87435833C>G, hg38,16:g.87402227C>G",0.415,,,0.0000039767440011,,,,3870023,Uncertain significance,not specified,1,,,,,, -59,51,K,,,,Ubq,,,Ac,,,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, +56,49,K,N,,,Ubq,,,Ac,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,"cBioPortal,COSMIC","mixed_allen_2018, skcm_dfci_2015","Cutaneous Melanoma, Mixed Cancer Types","hg19,16:87435831-87435831, hg38,16:87402225-87402225","hg19,16:g.87435831A>C, hg38,16:g.87402225A>C",0.495,skin,malignant_melanoma,,,,,,,,,,,,,, +57,50,T,I,P,,,,,,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,COSMIC,,,"hg38,16:87402227-87402227","hg38,16:g.87402227C>T",0.502,"upper_aerodigestive_tract, mouth, gingiva","carcinoma, squamous_cell_carcinoma",,,,,,,,,,,,,, +58,50,T,R,P,,,,,,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,ClinVar,,,"hg19,16:87435833-87435833, hg38,16:87402227-87402227","hg19,16:g.87435833C>G, hg38,16:g.87402227C>G",0.415,,,0.0000039767440011,,,,3870023,Uncertain significance,not specified,1,,,,,, +59,51,K,,,,Ubq,,,Ac,,Gly,,,PhosphoSite,"FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 60,52,F,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 61,53,L,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, 62,54,V,,,,,,,,,,,,,"PP4 EVH1-binding docking motifs (DOC_PP4_FxxP_1), 52-55, ELM|Arc N-lobe binding ligand (LIG_Arc_Nlobe_1), 54-58, ELM|FHA phosphopeptide ligands (LIG_FHA_1), 48-54, ELM",,,,,,,,,,,,,,,,,,,,,,, @@ -74,7 +74,7 @@ 72,62,E,,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 73,63,L,F,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,COSMIC,,,"hg38,16:87402265-87402265","hg38,16:g.87402265C>T",0.293,"skin, head_neck","malignant_melanoma, nodular",,,,,,,,,,,,,, 74,64,I,,,,,,,,,,,,,"NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, -75,65,K,E,,,Ubq,,,,,,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,"cBioPortal,COSMIC",coadread_genentech,Colorectal Adenocarcinoma,"hg19,16:87435877-87435877, hg38,16:87402271-87402271","hg19,16:g.87435877A>G, hg38,16:g.87402271A>G",0.314,"large_intestine, colon","carcinoma, adenocarcinoma",0.0000278640235650,,,,,,,,,,,,, +75,65,K,E,,,Ubq,,,,,Gly,,,PhosphoSite,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,"cBioPortal,COSMIC",coadread_genentech,Colorectal Adenocarcinoma,"hg19,16:87435877-87435877, hg38,16:87402271-87402271","hg19,16:g.87435877A>G, hg38,16:g.87402271A>G",0.314,"large_intestine, colon","carcinoma, adenocarcinoma",0.0000278640235650,,,,,,,,,,,,, 76,66,I,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 77,67,I,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 67-70, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, 78,68,R,,,,,,,,,,,,,"MAPK docking motifs (DOC_MAPK_gen_1), 65-73, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 67-70, ELM|di Arginine retention/retrieving signal (TRG_ER_diArg_1), 68-70, ELM|NES Nuclear Export Signals (TRG_NES_CRM1_1), 62-77, ELM",,,,,,,,,,,,,,,,,,,,,,, diff --git a/docs/my_table.pdf b/docs/my_table.pdf index 1dfc701d..6ee3e9b0 100644 Binary files a/docs/my_table.pdf and b/docs/my_table.pdf differ diff --git a/docs/my_table_pancancer.pdf b/docs/my_table_pancancer.pdf index 63d13792..b5349897 100644 Binary files a/docs/my_table_pancancer.pdf and b/docs/my_table_pancancer.pdf differ