diff --git a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py index 60086260..a537b605 100644 --- a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py +++ b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.py @@ -10,9 +10,13 @@ # add AnnData input file option parser.add_argument( - "-i", "--input_anndata", help="AnnData input file", required=True + "-i", "--input", + help=( + "AnnData or table input file. Table input is meant for a single " + "comparison, not gene x cells" + ), + required=True ) - # add network input file option parser.add_argument( "-n", "--input_network", help="Network input file", required=True @@ -34,6 +38,28 @@ default=None, ) +# Column for stat to use when providing a table +parser.add_argument( + "--stat", + help="Stat to use when providing a table. Default is 'log2FC'.", + default="log2FC", +) +# Optional column for p-value or FDR in the table +parser.add_argument( + "--p_value_column", + required=False, + help="Column name in the table with p-values or FDRs.", + default=None, +) +# Optional column for FDR threshold when given a table +parser.add_argument( + "--p_value_threshold", + required=False, + type=float, + help="Column name in the table with FDRs.", + default=0.05 +) + # Column name in net with source nodes parser.add_argument( "-s", @@ -93,8 +119,15 @@ if args.output is None: raise ValueError("Please specify either -o or --output") -# read in the AnnData input file -adata = ad.read_h5ad(args.input_anndata) +# detect based on input file extension if the input file is AnnData or matrix +if args.input.endswith(".h5ad"): + input_type = "AnnData" +elif args.input.endswith(".tsv") or args.input.endswith(".csv"): + input_type = "matrix" +else: + raise ValueError( + "Invalid input file. Please provide a valid AnnData or matrix file." + ) # read in the input file network input file network = pd.read_csv(args.input_network, sep="\t") @@ -108,17 +141,32 @@ "Source, target, and weight columns are not present in the network" ) - print(type(args.min_n)) -if args.var_gene_symbols_field and args.var_gene_symbols_field in adata.var.columns: - # Storing index in a column called 'index_bak' - adata.var['index_bak'] = adata.var.index - adata.var.set_index(args.var_gene_symbols_field, inplace=True) +if input_type == "AnnData": + # read in the AnnData input file + adata = ad.read_h5ad(args.input) + + if args.var_gene_symbols_field and args.var_gene_symbols_field in adata.var.columns: + # Storing index in a column called 'index_bak' + adata.var['index_bak'] = adata.var.index + adata.var.set_index(args.var_gene_symbols_field, inplace=True) +else: + # read in the matrix input file, genes in rows and columns for stats + adata = pd.read_csv(args.input, sep="\t", index_col=0) + if args.stat not in adata.columns: + raise ValueError(f"Stat column {args.stat} not found in input table header.") + if args.p_value_column and args.p_value_column not in adata.columns: + raise ValueError( + f"P-value column {args.p_value_column} not found in input table header." + ) + if args.p_value_column and args.p_value_threshold is not None: + adata = adata[adata[args.p_value_column] <= args.p_value_threshold] + adata = adata[[args.stat]].T if args.method == "mlm": - dc.run_mlm( + res = dc.run_mlm( mat=adata, net=network, source=args.source, @@ -129,24 +177,19 @@ use_raw=args.use_raw, ) - if args.output is not None: - # write adata.obsm[mlm_key] and adata.obsm[mlm_pvals_key] to the - # output network files - combined_df = pd.concat( - [adata.obsm["mlm_estimate"], adata.obsm["mlm_pvals"]], axis=1 - ) - - # Save the combined dataframe to a file - combined_df.to_csv(args.output + ".tsv", sep="\t") - - # if args.activities_path is specified, generate the activities AnnData - # and save the AnnData object to the specified path - if args.activities_path is not None: - acts = dc.get_acts(adata, obsm_key="mlm_estimate") - acts.write_h5ad(args.activities_path) - elif args.method == "ulm": - dc.run_ulm( + res = dc.run_ulm( + mat=adata, + net=network, + source=args.source, + target=args.target, + weight=args.weight, + verbose=True, + min_n=args.min_n, + use_raw=args.use_raw, + ) +elif args.method == "consensus": + res = dc.run_consensus( mat=adata, net=network, source=args.source, @@ -157,18 +200,31 @@ use_raw=args.use_raw, ) - if args.output is not None: - # write adata.obsm[mlm_key] and adata.obsm[mlm_pvals_key] to the - # output network files +if args.output is not None: + # write adata.obsm[mlm_key] and adata.obsm[mlm_pvals_key] to the + # output network files + if input_type == "AnnData": combined_df = pd.concat( - [adata.obsm["ulm_estimate"], adata.obsm["ulm_pvals"]], axis=1 + [adata.obsm[f"{args.method}_estimate"], + adata.obsm[f"{args.method}_pvals"]], axis=1 + ) + else: + tf_est, tf_pvals = res + combined_df = pd.DataFrame( + { + # index is written, so no need for the set names + f"{args.method}_estimate": tf_est.iloc[0], + f"{args.method}_pvals": tf_pvals.iloc[0], + } ) + # sort ascending on the p-values + combined_df.sort_values(by=f"{args.method}_pvals", inplace=True) - # Save the combined dataframe to a file - combined_df.to_csv(args.output + ".tsv", sep="\t") + # Save the combined dataframe to a file + combined_df.to_csv(args.output + ".tsv", sep="\t") - # if args.activities_path is specified, generate the activities AnnData - # and save the AnnData object to the specified path - if args.activities_path is not None: - acts = dc.get_acts(adata, obsm_key="ulm_estimate") - acts.write_h5ad(args.activities_path) +# if args.activities_path is specified, generate the activities AnnData +# and save the AnnData object to the specified path +if args.activities_path is not None and input_type == "AnnData": + acts = dc.get_acts(adata, obsm_key=f"{args.method}_estimate") + acts.write_h5ad(args.activities_path) diff --git a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml index e8010f37..0154293a 100644 --- a/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml +++ b/tools/tertiary-analysis/decoupler/decoupler_pathway_inference.xml @@ -1,4 +1,4 @@ - + of functional genesets/pathways for scRNA-seq data. @@ -6,109 +6,165 @@ decoupler + #if $inp.format == 'h5ad': + #set $input_fname = "input.h5ad" + #else: + #set $input_fname = "input.tsv" + #end if + ln -s '$input' '$input_fname'; + python '$__tool_directory__/decoupler_pathway_inference.py' - -i '$input_anndata' + -i '$input_fname' -n '$input_network_file' --min_n "$min_n" --method '$method' - $use_raw + --source '$source' --target '$target' --weight '$weight' - #if $gene_symbols_field: - --var_gene_symbols_field '$gene_symbols_field' + #if str($inp.format) == "tabular": + #if $inp.stat_field: + --stat "${inp.stat_field}" + #end if + #if $inp.p_value_column: + --p_value_column "${inp.p_value_column}" + --p_value_threshold "${inp.p_value_threshold}" + #end if + #else: + #if $inp.gene_symbols_field: + --var_gene_symbols_field "${inp.gene_symbols_field}" + #end if + #if $inp.use_raw: + ${inp.use_raw} + #end if + #if $inp.write_activities_path: + ${inp.write_activities_path} + #end if #end if --output "inference" - $write_activities_path + - - - + + + + + + + + + + + + + + + + + + + + - - - - - - + + + - write_activities_path + inp['format'] == "h5ad" and inp['write_activities_path'] is True - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + **What it does** @@ -119,34 +175,62 @@ Usage **Description** -This tool extracts pathway activity inference using decoupler. +This tool extracts pathway activity inference using decoupler. For more information on the underlying algorithms, +the `decoupler documentation`_ , in particular the Pathway Activity +and Transcription factor activity inference sections. + +.. _`decoupler documentation`: https://decoupler-py.readthedocs.io/en/latest/ + +**Input** + +The tool accepts two types of input files: -**Input** +1. An AnnData object in H5AD format: -The input file should be an AnnData object in H5AD format. The tool accepts an H5AD file containing raw or normalized data. + - The H5AD file can contain raw or normalized data. + - You can specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter. + - Minimum of targets per source can be specified using "min_n". -The tool also takes network file containing a collection of pathways and their target genes, with weights for each interaction. - Example: - ``` - source target weight - 0 T1 G01 1.0 - 1 T1 G02 1.0 - 2 T1 G03 0.7 - 3 T2 G04 1.0 - 4 T2 G06 -0.5 - ``` +2. A tabular file with differential expression data: -You can also specify whether to use the raw data in the AnnData object instead of the X matrix using the "use_raw" parameter and Minimum of targets per source using "min_n". + - The file should have genes in rows (and the first column by the gene symbols). + - The file needs a header, that is, columns names for every column. + - Columns must include at least fields similar to log2FC and a p-value or FDR field. + - If this file is provided, the tool will score each source in the network file according to the differential expression of the provided genes. + +The tool also requires a network file containing a collection of pathways and their target genes, with weights for each interaction. + +Example of a network file: + ++---------+--------+--------+ +| source | target | weight | ++=========+========+========+ +| T1 | G01 | 1.0 | ++---------+--------+--------+ +| T1 | G02 | 1.0 | ++---------+--------+--------+ +| T1 | G03 | 0.7 | ++---------+--------+--------+ +| T2 | G04 | 1.0 | ++---------+--------+--------+ +| T2 | G06 | -0.5 | ++---------+--------+--------+ **Output** -The tool outputs an AnnData object containing the scores in the "obs" field, and tab-separated text files containing the scores for each cell. +Depending on the input file type, the tool outputs: + +- If an AnnData file is used: -If the "write_activities_path" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file. -If the "write_inference" parameter is set to "true", the tool will output a tab-separated text file containing the scores for each cell. + - An AnnData object containing the scores in the "obs" field. + - Tab-separated text files containing the scores for each cell. + - If the "write_activities_path" parameter is set to "true", the tool will write the modified AnnData object to an H5AD file. + - If the "write_inference" parameter is set to "true", the tool will output a tab-separated text file containing the scores for each cell. +- If a tabular differential expression file is used: + - A tab-separated text file where each source in the network file is scored according to the differential expression of the provided genes. diff --git a/tools/tertiary-analysis/decoupler/test-data/diff_exp_result.tab b/tools/tertiary-analysis/decoupler/test-data/diff_exp_result.tab new file mode 100644 index 00000000..7bec6462 --- /dev/null +++ b/tools/tertiary-analysis/decoupler/test-data/diff_exp_result.tab @@ -0,0 +1,16407 @@ +Gene log2FoldChange pvalue padj +DOK6 0.51 1.861e-08 0.0003053 +TBX5 -2.129 5.655e-08 0.0004191 +SLC32A1 0.9003 7.664e-08 0.0004191 +IFITM1 -1.687 3.735e-06 0.006809 +NUP93 0.3659 3.373e-06 0.006809 +EMILIN2 1.534 2.976e-06 0.006809 +TPX2 -0.9974 2.097e-06 0.006809 +LAMA2 -1.425 2.39e-06 0.006809 +CAV2 -1.052 3.213e-06 0.006809 +TNN -1.658 8.973e-06 0.01472 +POU3F4 1.181 1.062e-05 0.01584 +COL13A1 -1.647 1.394e-05 0.01592 +IFITM3 -1.61 1.202e-05 0.01592 +SHISA3 -1.477 1.31e-05 0.01592 +LOC285954 1.05 1.456e-05 0.01592 +VEPH1 1.137 2.211e-05 0.02267 +ARHGAP29 -1.526 3.675e-05 0.03547 +KIAA1755 -1.562 3.972e-05 0.0362 +LAMC3 -1.563 4.29e-05 0.03704 +ITM2A -1.398 4.972e-05 0.04078 +DTHD1 1.54 5.594e-05 0.04371 +RBMS1 -0.9139 6.688e-05 0.04988 +CEBPD -1.202 7.859e-05 0.05606 +DMBX1 -1.425 9.529e-05 0.06486 +PAPLN -1.253 9.883e-05 0.06486 +ADM -1.357 0.0001089 0.06872 +COL2A1 -1.187 0.0001424 0.07794 +HS3ST3A1 -1.004 0.0001388 0.07794 +DYSF -1.03 0.0001425 0.07794 +PI16 1.495 0.0001297 0.07794 +CDC42EP5 -1.355 0.0001581 0.08146 +SLC12A8 -0.9425 0.0001589 0.08146 +ZNF391 -1.024 0.0001913 0.09512 +GALNTL2 1.075 0.0002298 0.1109 +C4orf45 1.288 0.0002472 0.1159 +KIF18B -0.8849 0.0002551 0.1162 +KIF20A -0.9505 0.0002972 0.1318 +PDE1B 1.053 0.0003356 0.1449 +BCAN 1.117 0.0003698 0.1477 +APLNR -1.365 0.000378 0.1477 +CILP -1.11 0.0003582 0.1477 +TEC -1.373 0.0003701 0.1477 +KLF5 -0.8177 0.0004159 0.1578 +ACSS2 -0.5578 0.0004232 0.1578 +RAPGEF2 0.3371 0.0004513 0.1645 +C1orf51 -0.6451 0.0005237 0.1665 +IGF2-AS1 -1.235 0.0005835 0.1665 +RPLP0P2 -1.096 0.0005689 0.1665 +COTL1 -0.7376 0.0005886 0.1665 +MYO1D -0.8454 0.0005529 0.1665 +CIAO1 0.2695 0.000522 0.1665 +POU3F3 0.6857 0.000588 0.1665 +CFLAR -0.9694 0.0005598 0.1665 +BHLHE40 -1.127 0.0004785 0.1665 +PLSCR4 -1.317 0.0004978 0.1665 +HECW1 0.5135 0.0005373 0.1665 +KCNQ3 1.147 0.000483 0.1665 +TIMP1 -1.15 0.0005267 0.1665 +CAV1 -1.115 0.0006722 0.1869 +LTBP4 -0.8186 0.0006991 0.1912 +HDAC1 -0.4542 0.0007203 0.1937 +HSPG2 -1.218 0.0007963 0.1947 +CYR61 -1.102 0.0008071 0.1947 +MYOF -1.194 0.0007397 0.1947 +COL4A1 -1.252 0.0007866 0.1947 +NMB 0.8677 0.0007872 0.1947 +ICAM1 -1.144 0.0007795 0.1947 +NOTCH3 -0.7585 0.0007529 0.1947 +MPPED2 0.5135 0.0008344 0.1984 +COL9A1 -0.9755 0.0008905 0.2087 +ACSF2 -1.142 0.0009448 0.2183 +KTN1 -0.3119 0.0009652 0.2199 +ITPR1 -1.118 0.00102 0.226 +PRPS2 -0.722 0.00101 0.226 +FAM180B 1.249 0.001146 0.2399 +POU2F3 -1.273 0.001114 0.2399 +COL5A2 -1.262 0.001155 0.2399 +ZSWIM3 0.438 0.001143 0.2399 +CADM2 0.643 0.001102 0.2399 +ARHGEF17 -0.5462 0.001214 0.2453 +SSC5D -1.126 0.001229 0.2453 +NRN1 0.8605 0.001241 0.2453 +PLAT -1.103 0.001226 0.2453 +SFXN2 -0.8373 0.00126 0.2456 +FMNL2 -0.2466 0.001276 0.2456 +ADAMTS3 -0.6153 0.001288 0.2456 +ADAMTS19 -1.199 0.001348 0.2543 +SH3BP1 -0.9641 0.001367 0.2548 +LEFTY2 -1.225 0.001414 0.2578 +EHBP1 0.3191 0.001414 0.2578 +UAP1L1 -1.113 0.001454 0.2622 +RAB27A -1.073 0.001516 0.2702 +ZNF213 0.3028 0.001604 0.28 +TOMM34 -0.4213 0.001596 0.28 +PERP -0.914 0.001672 0.2888 +OSMR -1.226 0.001749 0.2988 +CDCA3 -0.7986 0.001911 0.3119 +GPR179 0.8394 0.001972 0.3119 +TMC6 -1.078 0.001977 0.3119 +STXBP5L 0.6711 0.001936 0.3119 +HSPA1L 0.8842 0.001851 0.3119 +PLIN2 -0.604 0.001866 0.3119 +GSN -1.117 0.001977 0.3119 +F8A1 0.9911 0.00191 0.3119 +SLC27A6 -1.196 0.001998 0.3121 +COL4A2 -1.013 0.002192 0.3157 +WFDC1 -1.162 0.002149 0.3157 +DSEL 0.6867 0.002194 0.3157 +DOCK6 -0.8158 0.002172 0.3157 +MAN2B1 -0.4688 0.002099 0.3157 +NFKBIZ -0.888 0.002132 0.3157 +OCIAD2 0.7605 0.002108 0.3157 +REST -0.5478 0.002073 0.3157 +ANXA5 -0.8639 0.002075 0.3157 +TRIM13 0.3688 0.002254 0.3216 +ANLN -0.7229 0.002306 0.3261 +AP1S3 -0.8107 0.002352 0.3271 +LOC100859930 0.9008 0.002343 0.3271 +STK17B -0.887 0.00238 0.3281 +BHLHB9 0.4738 0.002441 0.3337 +IL1R1 -1.185 0.00248 0.3362 +CSDA -0.7633 0.002833 0.35 +POSTN -1.176 0.002706 0.35 +HHIPL1 0.8127 0.002742 0.35 +APBA2 0.4314 0.002752 0.35 +CBLN1 1.066 0.002768 0.35 +ALPK2 -1.108 0.002789 0.35 +NFATC2 -1.108 0.002726 0.35 +CN5H6.4 0.7852 0.002792 0.35 +ABHD14B -1.03 0.002859 0.35 +COL8A1 -1.171 0.002841 0.35 +HCG11 -0.8357 0.002844 0.35 +RUNX2 -0.88 0.002632 0.35 +EPB41L2 -0.9145 0.002832 0.35 +COL11A1 -1.145 0.002903 0.3528 +PODN -1.155 0.003085 0.3722 +NET1 -1.015 0.00311 0.3724 +IL13RA1 -1.106 0.003139 0.3731 +RNF207 -0.7995 0.003239 0.3798 +TRPM2 1.05 0.003246 0.3798 +SDF2L1 -0.4649 0.003298 0.3798 +SLCO2A1 -1.094 0.003293 0.3798 +DACT2 -1.06 0.00331 0.3798 +DCXR -0.4101 0.003335 0.38 +BCAM -0.8227 0.003423 0.3873 +FAM46B -1.002 0.00347 0.39 +FOXL1 -1.136 0.003579 0.3965 +SMTN -0.7131 0.003625 0.3965 +SLC6A1 0.7104 0.003616 0.3965 +YY2 -0.5988 0.003612 0.3965 +DEPDC1 -0.755 0.003704 0.3999 +HEPACAM2 1.116 0.003727 0.3999 +WBP5 -0.8485 0.003729 0.3999 +SPSB1 -1.05 0.003878 0.4105 +KIF23 -0.7154 0.003953 0.4105 +C1QL1 -1.072 0.003907 0.4105 +CBLN2 1.072 0.003934 0.4105 +LOC100505806 -1.069 0.003912 0.4105 +POU3F1 0.7912 0.004163 0.4116 +RGS8 0.9341 0.0043 0.4116 +GAD2 0.7494 0.004273 0.4116 +PKP2 -0.9689 0.004316 0.4116 +KIAA0564 -0.4253 0.004323 0.4116 +PIF1 -0.9292 0.004484 0.4116 +OR1F1 0.8391 0.004052 0.4116 +RRN3 0.3764 0.00431 0.4116 +CORO1A 0.4844 0.004098 0.4116 +CRISPLD2 -1.115 0.004242 0.4116 +TOP2A -0.7962 0.004366 0.4116 +ANKRD12 0.3062 0.004161 0.4116 +DHDH -0.811 0.004357 0.4116 +ZNF274 0.3354 0.004118 0.4116 +DPP4 -1.127 0.004023 0.4116 +TMEM169 0.7379 0.004108 0.4116 +CMTM8 -0.7701 0.004417 0.4116 +LAMP3 -0.9384 0.004515 0.4116 +SYNJ2 -0.9266 0.004504 0.4116 +DPY19L2P3 1.061 0.00448 0.4116 +TSC22D4 -0.5131 0.00443 0.4116 +AR -0.5979 0.00436 0.4116 +LOC339862 -1.109 0.004578 0.415 +CCDC152 0.9749 0.004621 0.4165 +NQO2 -0.6663 0.004716 0.4228 +CMTM5 1.096 0.004868 0.4341 +SERPING1 -0.8202 0.004974 0.4411 +TLCD2 -0.9392 0.005095 0.4494 +ATXN7L3B 0.3532 0.005133 0.4503 +APOE -0.9273 0.005183 0.4523 +GPC3 -1.073 0.005233 0.4542 +IRF1 -0.8166 0.00527 0.455 +GNG2 0.3508 0.005368 0.4611 +EPHX1 -0.5381 0.005794 0.4656 +CLEC2D -0.8191 0.005714 0.4656 +PTPRB -1.079 0.005753 0.4656 +NFATC4 -0.93 0.005692 0.4656 +LGALS3 -0.9472 0.005809 0.4656 +OTX2 0.8839 0.005746 0.4656 +UACA -1.058 0.005562 0.4656 +HAPLN3 -0.9001 0.005753 0.4656 +MYO5B -0.982 0.005461 0.4656 +PVRL3 -0.4554 0.005817 0.4656 +PRDM6 -1.068 0.005688 0.4656 +PDLIM7 -0.7154 0.005623 0.4656 +TSPYL4 0.3561 0.005811 0.4656 +CHRM2 0.9253 0.005564 0.4656 +PMEL -1.007 0.005987 0.4666 +GLIPR1 -1.05 0.006001 0.4666 +NLRC5 -0.9957 0.005976 0.4666 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-0.9248 0.01834 0.69 +PDGFRB -0.9184 0.01853 0.69 +FKBP5 -0.7347 0.01841 0.69 +AGBL3 0.5843 0.01861 0.69 +MNX1 0.921 0.01864 0.69 +PHKA2 -0.4551 0.01855 0.69 +CCBL2 -0.3365 0.01892 0.6925 +CLIC5 -0.9123 0.01883 0.6925 +WDR67 -0.3832 0.01887 0.6925 +SLC38A5 -0.7194 0.01895 0.6925 +KLF4 -0.8767 0.01907 0.6951 +HSD17B11 -0.6032 0.0192 0.6985 +SLC2A3 -0.5111 0.0193 0.7005 +CSDAP1 -0.7114 0.01946 0.7046 +SBNO2 -0.3452 0.01955 0.7064 +LRRC4C 0.5704 0.01962 0.7074 +ATL3 -0.5278 0.01975 0.7074 +C1S -0.9056 0.01966 0.7074 +PLAUR -0.8162 0.01974 0.7074 +LOC256021 0.6774 0.01988 0.709 +EID2B 0.4332 0.01987 0.709 +MTA3 -0.4227 0.02009 0.7151 +BSG -0.2869 0.02023 0.7167 +LAMP2 -0.2974 0.02022 0.7167 +ATHL1 -0.9069 0.02033 0.7179 +AHNAK -0.7987 0.02044 0.7179 +IGFBP5 -0.9055 0.02035 0.7179 +MBOAT1 -0.7067 0.02044 0.7179 +EGFR -0.6912 0.02048 0.7179 +FRAT1 0.4904 0.02073 0.7201 +TBX10 -0.9015 0.02084 0.7201 +KCNA6 0.4245 0.02068 0.7201 +MATN3 -0.8883 0.02079 0.7201 +LTBP1 -0.8212 0.02081 0.7201 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0.9251 +PVRL3-AS1 0.6451 0.06801 0.9251 +TAGLN3 0.4329 0.06554 0.9251 +BOC -0.6256 0.06355 0.9251 +GYG1 -0.3685 0.06421 0.9251 +NAALADL2 -0.6888 0.0651 0.9251 +LEPREL1 -0.7291 0.0615 0.9251 +PRKG2 -0.6991 0.06468 0.9251 +CYP4V2 0.5012 0.06519 0.9251 +C6 -0.6988 0.06235 0.9251 +ISOC1 -0.5486 0.0642 0.9251 +PCDHB10 0.3254 0.06221 0.9251 +ANXA6 -0.6452 0.06552 0.9251 +KIF4B -0.5101 0.06523 0.9251 +PRR7 0.1904 0.06493 0.9251 +LOC729678 0.6278 0.06551 0.9251 +HIST1H3J -0.6119 0.06763 0.9251 +ZBTB22 0.2669 0.06404 0.9251 +KIFC1 -0.549 0.06264 0.9251 +TBP 0.2407 0.0661 0.9251 +PMS2CL 0.3408 0.06648 0.9251 +FKBP14 -0.6002 0.06604 0.9251 +FKBP9 -0.4174 0.06186 0.9251 +GRM3 0.6129 0.06304 0.9251 +EPHB4 -0.6453 0.06787 0.9251 +LRRN3 0.5473 0.068 0.9251 +KIAA1147 0.257 0.06708 0.9251 +FAM115A 0.2185 0.06468 0.9251 +PDIA4 -0.4169 0.06375 0.9251 +ZNF775 0.2417 0.06198 0.9251 +FAM110B 0.2576 0.0615 0.9251 +DMRT3 0.7178 0.06674 0.9251 +CDKN2B -0.7039 0.06592 0.9251 +TSTD2 0.2954 0.06597 0.9251 +PTGES -0.7016 0.06267 0.9251 +FIBCD1 -0.6829 0.06516 0.9251 +STARD8 -0.7074 0.06244 0.9251 +KLHL4 -0.6903 0.0657 0.9251 +SH2D1A -0.6782 0.06569 0.9251 +HLX -0.6728 0.06837 0.927 +FOSB -0.6318 0.06832 0.927 +AKR1C3 -0.7137 0.06854 0.9278 +NFE2L2 -0.3512 0.06853 0.9278 +TRIP10 -0.5324 0.06872 0.9279 +ZNF14 0.3806 0.06869 0.9279 +DAB2 -0.5142 0.06862 0.9279 +CCNE1 -0.4662 0.06905 0.9309 +CRTAP -0.5294 0.06906 0.9309 +MYBPHL -0.6574 0.06967 0.9317 +RAB13 -0.5093 0.07021 0.9317 +IFITM2 -0.7098 0.06986 0.9317 +WEE1 -0.349 0.07071 0.9317 +LIN7C 0.3113 0.07001 0.9317 +NEAT1 -0.5604 0.06935 0.9317 +PRICKLE1 -0.6021 0.06958 0.9317 +TNFRSF12A -0.525 0.07083 0.9317 +ROGDI 0.3456 0.06977 0.9317 +CLEC16A 0.197 0.06923 0.9317 +TRADD -0.6894 0.0708 0.9317 +ATXN7L3 0.2479 0.07036 0.9317 +COIL 0.2361 0.06995 0.9317 +SPAST 0.3323 0.07065 0.9317 +RQCD1 0.2386 0.07059 0.9317 +HDLBP -0.3856 0.07093 0.9317 +ZNF502 0.7101 0.06932 0.9317 +LRRC58 -0.3642 0.07076 0.9317 +C4orf48 0.2925 0.07013 0.9317 +HMX1 -0.702 0.07093 0.9317 +SLC39A8 -0.3564 0.06976 0.9317 +PARP8 0.26 0.07093 0.9317 +AGXT2L2 -0.4154 0.07086 0.9317 +HIST1H4K -0.6587 0.07053 0.9317 +MDFI -0.4686 0.0692 0.9317 +TFEB -0.5835 0.07031 0.9317 +SOBP 0.2902 0.0707 0.9317 +EPM2A 0.3081 0.0706 0.9317 +RASEF -0.7099 0.07028 0.9317 +TOR2A 0.1958 0.07037 0.9317 +EFNB1 -0.4579 0.07022 0.9317 +IRS4 -0.6417 0.07016 0.9317 +FMNL1 0.5174 0.07107 0.9322 +CABLES2 0.1954 0.07108 0.9322 +PALMD -0.7062 0.07154 0.933 +ARHGAP30 0.4733 0.07142 0.933 +SLC6A12 -0.6354 0.0716 0.933 +FBXL8 -0.669 0.0716 0.933 +MPP4 -0.6609 0.07149 0.933 +FAM169A 0.2892 0.07155 0.933 +POPDC3 -0.6543 0.07148 0.933 +PRKDC -0.3408 0.07144 0.933 +MTCP1NB -0.3672 0.07166 0.9331 +KLHL35 0.547 0.07195 0.9361 +LOC388630 -0.6851 0.07216 0.9373 +TERF2 0.2403 0.07216 0.9373 +PDIK1L 0.3225 0.07438 0.9393 +CDKN2C -0.5881 0.07417 0.9393 +STAM 0.2146 0.07258 0.9393 +CEP55 -0.5626 0.07374 0.9393 +OAT -0.3282 0.07472 0.9393 +DPYSL4 0.3403 0.07368 0.9393 +INCENP -0.4533 0.07294 0.9393 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0.07698 0.9434 +BASP1 0.4201 0.07695 0.9434 +NCAPH2 0.2371 0.07719 0.9445 +PLA1A -0.5791 0.07721 0.9445 +EGFLAM -0.6643 0.07726 0.9445 +CD151 -0.3897 0.0774 0.9449 +STX11 -0.677 0.07738 0.9449 +APRT -0.3698 0.07756 0.9456 +PTPN2 -0.342 0.07763 0.9456 +PRRT4 0.5432 0.07763 0.9456 +ARRDC2 -0.5913 0.0778 0.9469 +POLD4 -0.613 0.07788 0.9471 +LDLRAP1 -0.6823 0.07828 0.9475 +SYDE2 -0.558 0.07807 0.9475 +TP53BP2 -0.3194 0.07848 0.9475 +ADAM12 -0.5572 0.07815 0.9475 +GAL3ST2 0.6873 0.07821 0.9475 +CTNND2 0.2648 0.07819 0.9475 +TSPAN13 0.4076 0.0783 0.9475 +RPS2P32 0.6489 0.0784 0.9475 +SLC26A7 -0.6902 0.07843 0.9475 +C9orf7 0.2083 0.07848 0.9475 +CDCA8 -0.5135 0.0788 0.9479 +MKNK1 -0.2483 0.07956 0.9479 +TOMM40L 0.3821 0.0791 0.9479 +PTGS2 -0.6878 0.07897 0.9479 +DNAJC1 -0.4755 0.07904 0.9479 +TLL2 0.5684 0.07932 0.9479 +PSD 0.5206 0.07953 0.9479 +LIMA1 -0.4947 0.07919 0.9479 +RBMS2 -0.4759 0.07932 0.9479 +CKAP4 -0.3698 0.07866 0.9479 +EEF1DP3 0.6545 0.07897 0.9479 +TAX1BP3 -0.4054 0.07874 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