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Merge pull request #121 from Sage-Bionetworks/jbeck/AG-1144/transform…
…_gene_info_testing Jbeck/ag 1144/transform gene info testing
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16 changes: 16 additions & 0 deletions
16
tests/test_assets/gene_info/input/diff_exp_data_good_input.csv
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model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study | ||
Diagnosis,TCX,AD-CONTROL,ENSG00000001626,-0.384,-0.61,-0.157,1.1,-3.32,0.001,0.003,protein_coding,7.0,DOWN,CFTR,36.59,250188,ALL,MAYO | ||
Diagnosis,TCX,AD-CONTROL,ENSG00000001631,0.096,0.028,0.164,3.66,2.79,0.005,0.013,protein_coding,7.0,NONE,KRIT1,36.48,47198,ALL,MAYO | ||
,TCX,AD-CONTROL,ENSG00000001629,0.069,-0.034,0.171,6.84,1.32,0.188,0.267,protein_coding,7.0,NONE,ANKIB1,36.83,155410,ALL,MAYO | ||
Diagnosis,,AD-CONTROL,ENSG00000001460,-0.043,-0.134,0.048,4.53,-0.92,0.357,0.452,protein_coding,1.0,NONE,,44.09,59936,ALL,MAYO | ||
Diagnosis,TCX,,ENSG00000000419,-0.011,-0.073,0.052,4.98,-0.34,0.737,0.799,protein_coding,20.0,NONE,DPM1,39.85,23689,ALL,MAYO | ||
Diagnosis,IFG,AD-CONTROL,ENSG00000000419,-0.088,-0.182,0.007,4.32,-1.82,0.069,0.155,,20.0,NONE,DPM1,39.85,23689,ALL,MSSM | ||
Diagnosis,IFG,,ENSG00000001629,0.08,0.007,0.154,7.93,2.16,0.031,0.085,protein_coding,,NONE,ANKIB1,36.83,155410,ALL,MSSM | ||
Diagnosis,IFG,AD-CONTROL,ENSG00000001460,-0.034,-0.114,0.046,3.81,-0.84,0.4,0.554,protein_coding,1.0,,STPG1,44.09,59936,,MSSM | ||
Diagnosis,IFG,AD-CONTROL,ENSG00000001631,-0.029,-0.095,0.037,4.12,-0.86,0.392,0.547,protein_coding,7.0,NONE,KRIT1,36.48,47198,ALL, | ||
Diagnosis,IFG,AD-CONTROL,ENSG00000001626,0.026,-0.128,0.179,3.01,0.33,0.741,0.834,protein_coding,7.0,NONE,,36.59,250188,ALL,MSSM | ||
Diagnosis,DLPFC,AD-CONTROL,ENSG00000001626,-0.143,-0.343,0.058,-0.3,-1.39,0.163,0.296,protein_coding,7.0,NONE,CFTR,36.59,250188,ALL, | ||
Diagnosis,DLPFC,AD-CONTROL,ENSG00000000419,-0.088,-0.131,-0.045,3.93,-4.03,0.0,0.001,protein_coding,20.0,NONE,DPM1,39.85,23689,ALL,ROSMAP | ||
Diagnosis,DLPFC,AD-CONTROL,ENSG00000001629,0.084,0.035,0.133,6.65,3.39,0.001,0.005,protein_coding,7.0,NONE,ANKIB1,36.83,155410,ALL,ROSMAP | ||
Diagnosis,DLPFC,AD-CONTROL,ENSG00000001460,-0.04,-0.092,0.012,4.02,-1.51,0.131,0.252,protein_coding,1.0,NONE,STPG1,44.09,59936,ALL,ROSMAP | ||
Diagnosis,DLPFC,AD-CONTROL,ENSG00000001631,-0.028,-0.07,0.014,2.94,-1.32,0.187,0.327,protein_coding,7.0,NONE,KRIT1,36.48,47198,ALL,ROSMAP |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/diff_exp_data_type_error.csv
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model,tissue,comparison,ensembl_gene_id,logfc,ci_l,ci_r,aveexpr,t,p_value,adj_p_val,gene_biotype,chromosome_name,direction,hgnc_symbol,percentage_gc_content,gene_length,sex,study | ||
Diagnosis,TCX,AD-CONTROL,ENSG00000001626,-0.384,-0.61,-0.157,1.1,-3.32,0.001,string_value,protein_coding,7.0,DOWN,CFTR,36.59,250188,ALL,MAYO | ||
Diagnosis,TCX,AD-CONTROL,ENSG00000001631,0.096,0.028,0.164,3.66,2.79,0.005,0.013,protein_coding,7.0,NONE,KRIT1,36.48,47198,ALL,MAYO |
6 changes: 6 additions & 0 deletions
6
tests/test_assets/gene_info/input/druggability_good_input.csv
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ensembl_gene_id,sm_druggability_bucket,safety_bucket,feasibility_bucket,abability_bucket,new_modality_bucket,tissue_engagement_bucket,pharos_class,classification,safety_bucket_definition,feasibility_bucket_definition,abability_bucket_definition,new_modality_bucket_definition,tissue_engagement_bucket_definition | ||
ENSG00000000005,7,4,4,3,4,4,Tbio,,Safety definition 1,Feasibility definition 1,Abability definition 1,Modaility definition 1,Tissue engagement definition 1 | ||
ENSG00000001036,1,3,5,1,4,2,Tchem,Classification 2,,Feasibility definition 2,Abability definition 2,Modaility definition 2,Tissue engagement definition 2 | ||
ENSG00000000460,13,3,5,3,4,4,Tdark,Classification 3,Safety definition 3,,,Modaility definition 3,Tissue engagement definition 3 | ||
ENSG00000000971,3,4,3,1,4,5,Tbio,Classification 4,Safety definition 4,Feasibility definition 4,Abability definition 4,,Tissue engagement definition 4 | ||
ENSG00000001084,1,5,3,3,4,2,,Classification 5,Safety definition 5,Feasibility definition 5,Abability definition 5,Modaility definition 5, |
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ensembl_gene_id,is_eqtl | ||
ENSG00000000419,True | ||
ENSG00000000971,True | ||
ENSG00000001460,True | ||
ENSG00000001626,True | ||
ENSG00000161149, | ||
ENSG00000001517,False |
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ensembl_gene_id,is_eqtl | ||
ENSG00000000419,True | ||
ENSG00000000971,True | ||
ENSG00000000419,True |
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7 changes: 7 additions & 0 deletions
7
tests/test_assets/gene_info/input/genes_biodomains_good_input.csv
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biodomain,abbr,label,color,go_id,goterm_name,n_symbol,symbol,ensembl_gene_id | ||
Synapse,Sy,Synapse [Sy],#329a33,GO:0005102,signaling receptor binding,362.0,TNMD,ENSG00000000005 | ||
Proteostasis,Pr,Proteostasis [Pr],#c8b269,,endopeptidase activity,73.0,TNMD,ENSG00000000005 | ||
Apoptosis,Ap,Apoptosis [Ap],,GO:0006915,apoptotic process,577.0,DPM1,ENSG00000000419 | ||
Structural Stabilization,,,#ff9a9a,GO:0030863,cortical cytoskeleton,21.0,SCYL3,ENSG00000000457 | ||
Synapse,Sy,Synapse [Sy],#329a33,GO:0034704,,,TNMD,ENSG00000000005 | ||
,Sy,Synapse [Sy],#329a33,GO:0034704,,,TNMD,ENSG00000000005 |
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ensembl_gene_id,hgnc_symbol | ||
ENSG00000000419,ADAMTS1 | ||
ENSG00000000460,APH1B | ||
ENSG00000000971, | ||
ENSG00000001084,UNC5CL | ||
ENSG00000001460,ICA1 | ||
,ICA1 |
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ensembl_gene_id,hgnc_symbol | ||
ENSG00000000419,ADAMTS1 | ||
ENSG00000000460,APH1B | ||
ENSG00000000460, |
11 changes: 11 additions & 0 deletions
11
tests/test_assets/gene_info/input/median_expression_good_input.csv
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ensembl_gene_id,min,first_quartile,median,mean,third_quartile,max,tissue | ||
ENSG00000000419,4.14,4.82,4.99,4.98,5.12,5.47,TCX | ||
ENSG00000000457,1.87,3.31,3.56,3.53,3.79,4.29,TCX | ||
ENSG00000000971,2.38,3.78,4.78,4.66,5.42,7.48, | ||
ENSG00000001036,2.55,3.42,3.69,3.67,3.9,4.69,TCX | ||
ENSG00000001631,2.39,3.43,3.58,3.56,3.71,4.0,TCX | ||
ENSG00000000419,2.46,3.81,4.11,4.11,4.4,5.85,DLPFC | ||
ENSG00000000971,1.75,3.69,4.33,4.38,4.99,8.17,DLPFC | ||
ENSG00000000419,2.43,3.82,4.17,4.13,4.5,5.35,IFG | ||
ENSG00000001036,2.04,3.44,3.64,3.63,3.86,4.8,IFG | ||
ENSG00000001631,3.07,3.75,3.88,3.88,4.01,4.42,IFG |
17 changes: 17 additions & 0 deletions
17
tests/test_assets/gene_info/input/proteomics_good_input.csv
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
DPM1|O60762,DPM1,O60762,ENSG00000000419,DLPFC,-0.001,0.109,-0.11,1.0,1.0 | ||
GCLC|P48506,GCLC,P48506,ENSG00000001084,DLPFC,0.172,0.241,0.104,0.0,0.0 | ||
CFH|P08603,CFH,P08603,ENSG00000000971,DLPFC,,,,, | ||
CYP51A1|Q16850,CYP51A1,Q16850,ENSG00000001630,DLPFC,,,,, | ||
DPM1|O60762,DPM1,O60762,ENSG00000000419,MFG,0.175,0.814,-0.463,0.784,1.0 | ||
GCLC|P48506,GCLC,P48506,ENSG00000001084,MFG,0.011,0.23,-0.207,0.991,1.0 | ||
CFH|P08603,CFH,P08603,ENSG00000000971,,0.005,0.8,-0.79,1.0,1.0 | ||
CYP51A1|Q16850,CYP51A1,Q16850,ENSG00000001630,MFG,,,,, | ||
DPM1|O60762,DPM1,,ENSG00000000419,TCX,-0.149,0.011,-0.309,0.073,0.383 | ||
GCLC|P48506,GCLC,P48506,ENSG00000001084,TCX,-0.043,0.042,-0.128,0.462,1.0 | ||
CFH|P08603,CFH,P08603,ENSG00000000971,TCX,,,,, | ||
CYP51A1|Q16850,CYP51A1,Q16850,ENSG00000001630,TCX,,,,, | ||
DPM1|O60762,DPM1,O60762,ENSG00000000419,AntPFC,0.052,0.215,-0.111,0.734,1.0 | ||
GCLC|P48506,,P48506,ENSG00000001084,AntPFC,-0.023,0.077,-0.123,0.848,1.0 | ||
CFH|P08603,CFH,P08603,ENSG00000000971,AntPFC,,,,, | ||
,CYP51A1,Q16850,ENSG00000001630,AntPFC,0.265,0.567,-0.037,0.099,0.565 |
7 changes: 7 additions & 0 deletions
7
tests/test_assets/gene_info/input/proteomics_srm_good_input.csv
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
CD2AP|Q9Y5K6,CD2AP,Q9Y5K6,ENSG00000001630,DLPFC,0.026,0.102,-0.05,0.696,0.952 | ||
,SNCA,P37840,ENSG00000001629,DLPFC,-0.026,0.028,-0.08,0.505,0.72 | ||
NDUFA7|O95182,,O95182,ENSG00000000419,DLPFC,-0.083,-0.034,-0.131,0.0,0.001 | ||
DIP2B|Q9P265,DIP2B,,ENSG00000001036,DLPFC,0.002,0.072,-0.068,0.997, | ||
VSNL1|P62760,VSNL1,P62760,ENSG00000000971,,-0.014,0.015,-0.042,0.493,0.718 | ||
SYT11|Q9BT88,SYT11,Q9BT88,ENSG00000000005,DLPFC,0.029,0.074,-0.016,0.281,0.496 |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/proteomics_srm_type_error.csv
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
CD2AP|Q9Y5K6,CD2AP,Q9Y5K6,ENSG00000001630,DLPFC,0.026,0.102,-0.05,0.696,string_value | ||
,SNCA,P37840,ENSG00000001629,DLPFC,-0.026,0.028,-0.08,0.505,0.72 |
7 changes: 7 additions & 0 deletions
7
tests/test_assets/gene_info/input/proteomics_tmt_good_input.csv
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
CYP51A1|A0A0C4DFL7,CYP51A1,A0A0C4DFL7,ENSG00000001630,DLPFC,-0.097,-0.025,-0.168,0.009,0.06 | ||
ANKIB1|Q9P2G1,ANKIB1,Q9P2G1,ENSG00000001629,,-0.023,-0.003,-0.044,0.027,0.124 | ||
,DPM1,H0Y368,ENSG00000000419,DLPFC,-0.032,-0.002,-0.062,0.038,0.153 | ||
FUCA2|Q9BTY2,,Q9BTY2,ENSG00000001036,DLPFC,-0.089,0.006,-0.184,0.066,0.213 | ||
CFH|P08603,CFH,P08603,ENSG00000000971,DLPFC,,0.156,-0.004,0.062,0.205 | ||
KRIT1|O00522,KRIT1,,ENSG00000001631,DLPFC,0.053,0.121,-0.015,0.128,0.319 |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/proteomics_tmt_type_error.csv
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
CYP51A1|A0A0C4DFL7,CYP51A1,A0A0C4DFL7,ENSG00000001630,DLPFC,-0.097,-0.025,-0.168,0.009,string_value | ||
ANKIB1|Q9P2G1,ANKIB1,Q9P2G1,ENSG00000001629,,-0.023,-0.003,-0.044,0.027,0.124 |
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uniqid,genename,uniprotid,ensembl_gene_id,tissue,log2_fc,ci_upr,ci_lwr,pval,cor_pval | ||
DPM1|O60762,DPM1,O60762,ENSG00000000419,DLPFC,-0.001,0.109,-0.11,1.0,string_value | ||
GCLC|P48506,GCLC,P48506,ENSG00000001084,DLPFC,0.172,0.241,0.104,0.0,0.0 |
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source,team,rank,ensembl_gene_id,hgnc_symbol,target_choice_justification,predicted_therapeutic_direction,data_used_to_support_target_selection,data_synapseid,study,input_data,validation_study_details,initial_nomination | ||
Source_1,Team_1,17-100,ENSG00000000005,TNMD,Justification 1,Prediction 1,Support 1,syn12345,Study_1,"Genetics, RNA, Protein, Clinical",,2018.0 | ||
Source_1,Team_2,,ENSG00000000419,DPM1,Justification 2,Prediction 2,Support 2,,Study_1,,Validation 2,2023.0 | ||
Source_2,Team_3,12,ENSG00000000419,DPM1,Justification 3,,Support 3,,Study_2,RNA,Validation 3,2022.0 | ||
Source_3,Team_4,1-10,ENSG00000000419,DPM1,,Prediction 4,Support 4,syn56789,Study_3,"Protein, Clinical",Validation 4,2018.0 | ||
Source_4,Team_5,,ENSG00000000457,SCYL3,Justification 5,Prediction 5,,,Study_3,RNA,Validation 5, |
6 changes: 6 additions & 0 deletions
6
tests/test_assets/gene_info/input/tep_adi_info_good_input.csv
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ensembl_gene_id,hgnc_symbol,is_adi,is_tep | ||
ENSG00000000005,TNMD,True,True | ||
ENSG00000000419,DPM1,,False | ||
ENSG00000001497,LAS1L,True, | ||
ENSG00000001084,GCLC,,True | ||
ENSG00000183791,ABCD,, |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/tep_adi_info_type_error_1.csv
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ensembl_gene_id,hgnc_symbol,is_adi,is_tep | ||
ENSG00000000005,,True,True | ||
ENSG00000000419,DPM1,,False |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/tep_adi_info_type_error_2.csv
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ensembl_gene_id,hgnc_symbol,is_adi,is_tep | ||
ENSG00000000005,TNMD,string_value,True | ||
ENSG00000000419,DPM1,,False |
3 changes: 3 additions & 0 deletions
3
tests/test_assets/gene_info/input/tep_adi_info_type_error_3.csv
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ensembl_gene_id,hgnc_symbol,is_adi,is_tep | ||
ENSG00000000005,TNMD,True,string_value | ||
ENSG00000000419,DPM1,,False |
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