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LINCS1与LINCS2数据库

LINCS1与LINCS2数据库

作者: 小贝学生信 | 来源:发表于2022-01-11 01:35 被阅读0次

    https://docs.google.com/document/d/1q2gciWRhVCAAnlvF2iRLuJ7whrGP6QjpsCMq1yWz7dU

    Part 1、LINCS Phase I L1000--GSE92742

    1、signature矩阵

    library(cmapR)
    library(tidyverse)
    
    gctx_demo = parse_gctx("GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx", 
                           cid=1:4, rid=1:4)
    gctx_demo@mat
         # CPC005_A375_6H:BRD-A85280935-003-01-7:10
    # 5720                                0.7737690
    # 466                                -0.8184680
    # 6009                                0.1895723
    # 2309                               -0.1460308
         # CPC005_A375_6H:BRD-A07824748-001-02-6:10
    # 5720                               -0.6455861
    # 466                                -0.8107487
    # 6009                                0.4590603
    # 2309                               -0.2246765
         # CPC004_A375_6H:BRD-K20482099-001-01-1:10
    # 5720                                -5.449666
    # 466                                  2.393775
    # 6009                                 1.279790
    # 2309                                 2.167868
         # CPC005_A375_6H:BRD-K62929068-001-03-3:10
    # 5720                                0.1934077
    # 466                                -0.5822433
    # 6009                               -0.1789770
    # 2309                               -1.1820246
    

    2、signature注释信息

    • 从GEO下载的顺序与上面gct矩阵的sig顺序不一致,需要调整与gct保持一致,方便后续取子集操作。
      如下是已经调整好的:
    sig_info = data.table::fread("Fine_phase1_sig_info_473647.csv",
                                 data.table = F)
    
    col_meta <- read_gctx_meta("GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx", dim="col")
    identical(col_meta$id, sig_info$sig_id)
    # [1] TRUE
    
    dim(sig_info)
    # [1] 473647     12
    t(sig_info[1,])
    #                 [,1]                                                                                                            
    # sig_id         "CPC005_A375_6H:BRD-A85280935-003-01-7:10"                                                                      
    # pert_id        "BRD-A85280935"
    # pert_iname     "quinpirole"                                                                                                    
    # pert_type      "trt_cp"                                                                                                        
    # cell_id        "A375"                                                                                                          
    # pert_dose      "10.0"                                                                                                          
    # pert_dose_unit "µM"                                                                                                            
    # pert_idose     "10 µM"                                                                                                         
    # pert_time      "6"                                                                                                             
    # pert_time_unit "h"                                                                                                             
    # pert_itime     "6 h"                                                                                                           
    # distil_id      "CPC005_A375_6H_X1_B3_DUO52HI53LO:K06|CPC005_A375_6H_X2_B3_DUO52HI53LO:K06|CPC005_A375_6H_X3_B3_DUO52HI53LO:K06"
    

    3、gene注释信息

    • 同上也需要调整顺序
    gene_info = data.table::fread("Fine_phase1_gene_info_12328.csv",
                                  data.table = F)
    
    row_meta <- read_gctx_meta("GSE92742_Broad_LINCS_Level5_COMPZ.MODZ_n473647x12328.gctx", dim="row")
    identical(as.integer(row_meta$id), gene_info$pr_gene_id)
    # [1] TRUE
    
    dim(gene_info)
    # [1] 12328     5
    t(gene_info[1,])
    #                 1                             
    # pr_gene_id     "5720"                          
    # pr_gene_symbol "PSME1"                         
    # pr_gene_title  "proteasome activator subunit 1"
    # pr_is_lm       "1"        # landmark    978                         
    # pr_is_bing     "1"        # landmark + best inferred gene   10174
    

    4、pertubation(化合物)注释信息

    • 可结合signature注释信息,做进一步筛选
    pert_info = data.table::fread("phase1_pert_info.csv")
    t(pert_info[1,])
    #                   [,1]    
    # V1               "1"     
    # pert_id          "56582" 
    # pert_iname       "AKT2"  
    # pert_type        "trt_oe"
    # is_touchstone    "0"     
    # inchi_key_prefix "-666"  
    # inchi_key        "-666"  
    # canonical_smiles "-666"  
    # pubchem_cid      "-666"  
    
    table(pert_info$pert_type) %>% sort(decreasing = T)
    # trt_cp          trt_sh      trt_sh.cgs      trt_sh.css 
    # 20413           18493            4345            3807 
    # trt_oe         trt_lig      trt_oe.mut      ctl_vector 
    # 3492             622             135              61 
    #...
    

    5、细胞系注释信息

    • 可结合signature注释信息,做进一步筛选
    cell_info = data.table::fread("phase1_cell_info.csv")
    t(cell_info[1,])
    #                         [,1]                
    # cell_id                 "A375"              
    # cell_type               "cell line"         
    # base_cell_id            "A375"              
    # precursor_cell_id       "-666"              
    # modification            "-666"              
    # sample_type             "tumor"             
    # primary_site            "skin"              
    # subtype                 "malignant melanoma"
    # original_growth_pattern "adherent"          
    # provider_catalog_id     "CRL-1619"          
    # original_source_vendor  "ATCC"              
    # donor_age               "54"                
    # donor_sex               "F"                 
    # donor_ethnicity         "-666"  
    
    table(cell_info$sample_type)
    # -666  normal primary   tumor 
    # 1      19       8      70
    

    6、signature干扰效应评价

    • Replicate Correlation Coefficient
    • signature strength
    • Transcriptional Activity Score
    sig_metrics = data.table::fread("phase1_sig_metrcs.csv")
    
    identical(sig_metrics$sig_id, col_meta$id)
    # [1] TRUE
    
    t(sig_metrcs[1,])
    # [,1]
    # sig_id                 "CPC005_A375_6H:BRD-A85280935-003-01-7:10"
    # pert_id                "BRD-A85280935"
    # pert_iname             "quinpirole"
    # pert_type              "trt_cp"
    # distil_cc_q75          "0.11"   (Replicate Correlation Coefficient)           
    # distil_ss              "2.84895" (signature strength)    
    # ngenes_modulated_up_lm "18"
    # ngenes_modulated_dn_lm "15"
    # tas                    "0.101169" (Transcriptional Activity Score)        
    # pct_self_rank_q25      "7.6087"
    # is_exemplar            "0"
    # distil_nsample         "3"
    

    Part 2、LINCS Phase II L1000--GSE70138

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