# HG changeset patch # User ebi-gxa # Date 1732880056 0 # Node ID 09c833d9b03b014ac25f8d4e70065a5c3e3768cb # Parent ef054892d47f8f792ab4acd9a4aa845fcf2b56a3 planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b581a5b4ba88c5bf06f6223ba9aec51a8564796c diff -r ef054892d47f -r 09c833d9b03b decoupler_pathway_inference.py --- a/decoupler_pathway_inference.py Wed Oct 30 14:26:40 2024 +0000 +++ b/decoupler_pathway_inference.py Fri Nov 29 11:34:16 2024 +0000 @@ -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 -r ef054892d47f -r 09c833d9b03b test-data/diff_exp_result.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/diff_exp_result.tab Fri Nov 29 11:34:16 2024 +0000 @@ -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 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-0.8999 0.01677 0.6753 +TMEM196 0.7006 0.01701 0.6753 +NOD1 -0.5152 0.01707 0.6753 +GLI3 -0.8242 0.01696 0.6753 +WBSCR27 -0.9343 0.01718 0.6753 +C7orf34 0.9318 0.01721 0.6753 +FRRS1 -0.8998 0.01774 0.676 +FAM19A3 -0.8923 0.01788 0.676 +CNIH3 -0.4817 0.01784 0.676 +MDK -0.7156 0.01749 0.676 +GXYLT1 -0.6944 0.01783 0.676 +CTDSP2 -0.5123 0.01765 0.676 +SIX4 -0.8657 0.01784 0.676 +SLCO3A1 0.4415 0.01784 0.676 +PTBP1 -0.4376 0.0178 0.676 +ZNF324 0.3139 0.01754 0.676 +COLEC11 -0.9194 0.01776 0.676 +APOBEC3B -0.9292 0.01771 0.676 +MAGEF1 0.3826 0.01768 0.676 +SHROOM2 0.5668 0.01763 0.676 +KIAA1217 -0.7442 0.01871 0.69 +ST8SIA1 0.3806 0.01869 0.69 +LOC338758 0.6997 0.01834 0.69 +LOC283731 -0.4064 0.01872 0.69 +LYSMD4 0.4181 0.01859 0.69 +CYP1B1 -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 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0.02134 0.7264 +PCDHGB4 -0.8844 0.02142 0.7277 +P2RX4 -0.3807 0.02159 0.7309 +LINC00574 0.7267 0.02161 0.7309 +BPI -0.8613 0.02171 0.7313 +ATP2B2 0.751 0.02167 0.7313 +CDCA2 -0.6352 0.0218 0.7328 +FGF8 -0.8835 0.02191 0.7338 +FAM198A -0.8977 0.02192 0.7338 +FMO2 -0.8029 0.0222 0.7401 +LOC642852 0.5471 0.02215 0.7401 +IGF2R -0.5322 0.02227 0.741 +TIGD3 0.6643 0.02236 0.7426 +GFPT2 -0.6006 0.02241 0.7429 +BCAS2 0.3073 0.02266 0.7431 +IQGAP3 -0.7145 0.02274 0.7431 +ZDHHC20 -0.3828 0.02266 0.7431 +ARID4A 0.2039 0.02278 0.7431 +SPHK1 -0.8455 0.02253 0.7431 +FAM110C -0.7952 0.02259 0.7431 +PXDN -0.7352 0.02275 0.7431 +THSD7B -0.5467 0.02268 0.7431 +PRUNE 0.2438 0.02292 0.7459 +ECE1 -0.7102 0.02311 0.7477 +CECR7 0.8781 0.02308 0.7477 +HTRA3 -0.8843 0.02303 0.7477 +WDR47 0.4054 0.0234 0.7537 +SLITRK5 0.4093 0.02345 0.7537 +AURKB -0.6811 0.02349 0.7537 +IGFBP4 -0.8858 0.02352 0.7537 +CDC25C -0.6363 0.02348 0.7537 +GPM6A 0.649 0.02357 0.7538 +BTBD19 -0.7584 0.02376 0.755 +GPR26 0.7615 0.02388 0.755 +SIAH3 0.7351 0.02393 0.755 +PLCB2 -0.8363 0.02385 0.755 +DNM1P35 0.6404 0.02389 0.755 +RRBP1 -0.8115 0.0238 0.755 +ACOT8 0.3293 0.02375 0.755 +OLFML2B -0.8708 0.02414 0.7572 +TROAP -0.7143 0.02411 0.7572 +WIPI1 -0.6362 0.02411 0.7572 +VOPP1 0.2574 0.02422 0.7584 +HES1 -0.5633 0.02436 0.7611 +FIBIN -0.8826 0.02444 0.7624 +KDELC2 -0.8298 0.02449 0.7625 +ERRFI1 -0.5181 0.02486 0.767 +ZNF26 0.2525 0.0249 0.767 +RAB20 -0.7225 0.02495 0.767 +CEP112 -0.5528 0.02496 0.767 +PDYN 0.8461 0.02487 0.767 +SEL1L3 -0.794 0.0249 0.767 +CENPE -0.581 0.02474 0.767 +LOC100505695 -0.8418 0.02506 0.7684 +ST3GAL6 0.3335 0.02515 0.7698 +PPPDE1 -0.3884 0.02552 0.7705 +CYFIP1 -0.4708 0.02549 0.7705 +SPAG5 -0.6341 0.02525 0.7705 +FSTL3 -0.3936 0.02544 0.7705 +DKKL1 -0.5961 0.02555 0.7705 +PLA2R1 -0.8383 0.02533 0.7705 +SH3RF2 -0.8594 0.02543 0.7705 +NEDD9 -0.5615 0.02537 0.7705 +LOC400940 0.7406 0.02573 0.7737 +NPR2 -0.6064 0.02575 0.7737 +CKS1B -0.6537 0.02617 0.778 +RNASEL 0.8586 0.02631 0.778 +KIAA1462 -0.8624 0.02641 0.778 +C10orf2 0.3805 0.02618 0.778 +PRKCDBP -0.8186 0.02624 0.778 +ZNF564 0.3025 0.02598 0.778 +LOC100506421 0.6526 0.02601 0.778 +SNED1 -0.8004 0.02611 0.778 +SGMS2 -0.8683 0.02638 0.778 +TMEM151B 0.4716 0.02635 0.778 +LOC100507341 0.6623 0.02622 0.778 +KIF2C -0.6374 0.02666 0.7837 +PRX -0.6445 0.02676 0.7854 +LOXL4 -0.8597 0.02686 0.7864 +STXBP6 0.6668 0.02689 0.7864 +FAM13A -0.4611 0.02712 0.7917 +IFITM10 0.6685 0.02744 0.7925 +CBFB -0.3576 0.02735 0.7925 +DKFZp566F0947 -0.8205 0.02736 0.7925 +MAGI2 0.4314 0.02741 0.7925 +NIPAL2 -0.7441 0.0274 0.7925 +GPRASP2 0.4453 0.02732 0.7925 +DPH3P1 -0.5664 0.02774 0.7999 +C1orf54 -0.5484 0.02801 0.8025 +LIG4 0.3168 0.02811 0.8025 +GREM1 -0.8574 0.02807 0.8025 +TPM4 -0.6659 0.028 0.8025 +OSBPL10 -0.7943 0.02789 0.8025 +HPS3 -0.3542 0.02812 0.8025 +ANP32B -0.4906 0.02825 0.8047 +FAM176B -0.6818 0.02966 0.8067 +HPCAL4 0.5034 0.02927 0.8067 +LEPRE1 -0.7027 0.03137 0.8067 +MCOLN3 -0.7816 0.02861 0.8067 +GBP3 -0.8426 0.03082 0.8067 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-0.8334 0.0328 0.8067 +CELF5 0.4393 0.03193 0.8067 +TMEM221 -0.7671 0.03202 0.8067 +WDR62 -0.5769 0.02965 0.8067 +ZNF570 0.2708 0.02949 0.8067 +SPRED3 0.6054 0.03154 0.8067 +RPL13A -0.6422 0.03157 0.8067 +BCL2L12 -0.4817 0.02883 0.8067 +CENPA -0.6156 0.03213 0.8067 +MTHFD2 -0.7685 0.03077 0.8067 +FAM176A -0.8313 0.03045 0.8067 +GCFC2 -0.344 0.02982 0.8067 +CAPG -0.8383 0.0296 0.8067 +EDAR -0.846 0.03099 0.8067 +BUB1 -0.5945 0.02946 0.8067 +ZRANB3 -0.5034 0.03047 0.8067 +SLC4A10 0.725 0.03287 0.8067 +WIPF1 -0.555 0.02846 0.8067 +CCDC141 -0.8347 0.02951 0.8067 +CCDC150 -0.5535 0.03183 0.8067 +ASXL1 -0.4027 0.03086 0.8067 +SS18L1 0.3675 0.03085 0.8067 +C22orf29 0.2474 0.03243 0.8067 +SMCR7L 0.1929 0.03016 0.8067 +GRIP2 0.8047 0.03072 0.8067 +GPR62 0.808 0.03283 0.8067 +MITF -0.7604 0.03019 0.8067 +FDCSP -0.8326 0.03137 0.8067 +ANXA2P1 -0.6149 0.0322 0.8067 +LHFPL2 -0.7202 0.03111 0.8067 +ERAP1 -0.4938 0.03164 0.8067 +MXD3 -0.6781 0.02998 0.8067 +TEAD3 -0.7435 0.02893 0.8067 +SP4 0.3326 0.03284 0.8067 +TRIL -0.7788 0.0308 0.8067 +STK17A -0.3401 0.02899 0.8067 +RARRES2 -0.844 0.02997 0.8067 +CHMP7 0.283 0.03105 0.8067 +ZNF703 -0.6856 0.03162 0.8067 +ST18 0.5283 0.03123 0.8067 +LOC100132891 -0.7824 0.03111 0.8067 +C8orf84 -0.7652 0.03183 0.8067 +ZFHX4 0.4288 0.03044 0.8067 +GDF6 -0.8041 0.03241 0.8067 +RANBP6 0.3012 0.03171 0.8067 +FAM189A2 -0.8114 0.0328 0.8067 +TNC -0.8197 0.03225 0.8067 +ZBTB6 0.3295 0.02968 0.8067 +RPL12 -0.5342 0.02943 0.8067 +GBGT1 -0.8343 0.03067 0.8067 +ARHGAP6 -0.8167 0.03244 0.8067 +SHROOM4 -0.645 0.03263 0.8067 +HDX 0.4208 0.03269 0.8067 +COL4A5 -0.7708 0.03259 0.8067 +GAB3 -0.7788 0.03107 0.8067 +B3GALNT2 -0.5213 0.03322 0.809 +ZNF142 0.2381 0.03314 0.809 +HEXB -0.4081 0.03323 0.809 +PPP1R3G -0.8344 0.03314 0.809 +MDFIC -0.6575 0.03324 0.809 +RXFP3 0.832 0.03336 0.8098 +PTTG3P -0.6051 0.03333 0.8098 +C1orf133 -0.7152 0.03375 0.8176 +TP53I13 -0.422 0.03379 0.8176 +SLC44A3 -0.7081 0.03438 0.8264 +C1orf115 -0.6315 0.03446 0.8264 +ANO4 -0.7486 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0.9251 +SLC8A2 0.5135 0.06325 0.9251 +FLT3LG -0.692 0.0649 0.9251 +TMEM214 -0.496 0.06786 0.9251 +PLB1 -0.7173 0.06319 0.9251 +EML4 -0.4048 0.06662 0.9251 +TEKT4 0.701 0.06517 0.9251 +FAHD2A -0.2582 0.06363 0.9251 +LIMS1 -0.5014 0.06794 0.9251 +POTEF -0.7024 0.06758 0.9251 +NCKAP5 -0.3493 0.06549 0.9251 +SERPINE2 -0.3999 0.06232 0.9251 +NYAP2 0.6993 0.06519 0.9251 +ZNF217 -0.5587 0.06492 0.9251 +CBLN4 0.5841 0.06282 0.9251 +USP25 -0.3405 0.06659 0.9251 +LHFPL4 0.5292 0.06225 0.9251 +VGLL4 -0.3355 0.06504 0.9251 +RBMS3 -0.6397 0.06258 0.9251 +ZNF167 0.4354 0.06685 0.9251 +SEMA3B -0.6083 0.0665 0.9251 +ROBO2 0.3634 0.06146 0.9251 +NIT2 -0.5819 0.06183 0.9251 +ABI3BP -0.7291 0.06193 0.9251 +DZIP3 0.3206 0.06691 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 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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 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0.07443 0.9393 +UNC45A -0.399 0.07369 0.9393 +QPRT -0.459 0.07395 0.9393 +FHOD1 -0.5817 0.07342 0.9393 +PMFBP1 -0.6728 0.07513 0.9393 +VPS53 0.2412 0.07388 0.9393 +GSG2 -0.5565 0.07526 0.9393 +DNAH2 0.5147 0.0737 0.9393 +MRM1 0.4208 0.07515 0.9393 +MPP2 0.354 0.07332 0.9393 +ITGB4 -0.6953 0.07405 0.9393 +CCDC68 -0.696 0.07529 0.9393 +SALL3 0.49 0.07403 0.9393 +TMC4 -0.5552 0.0751 0.9393 +ZNF329 0.2676 0.07305 0.9393 +ZNF324B 0.4072 0.07329 0.9393 +MAT2A 0.3537 0.0727 0.9393 +RND3 0.4659 0.07447 0.9393 +IL5RA 0.6958 0.07526 0.9393 +TUSC2 0.3129 0.07499 0.9393 +TACC3 -0.4554 0.07503 0.9393 +RGS12 0.2794 0.07467 0.9393 +KLHL8 0.2803 0.07494 0.9393 +CXXC4 0.3722 0.07323 0.9393 +RAB33B -0.3195 0.07345 0.9393 +LRP2BP 0.5095 0.0735 0.9393 +RIOK1 0.2755 0.07471 0.9393 +GUSB -0.289 0.07272 0.9393 +WNT16 -0.6902 0.07499 0.9393 +MTMR9 0.4022 0.07321 0.9393 +RB1CC1 0.1851 0.07324 0.9393 +LOC100130301 -0.6884 0.07526 0.9393 +ZHX2 -0.1906 0.07262 0.9393 +C8orf31 0.662 0.07311 0.9393 +PTPLAD2 -0.6807 0.07516 0.9393 +ANGPTL2 -0.6812 0.0727 0.9393 +XKR9 0.6838 0.07538 0.9397 +NPM3 -0.43 0.07558 0.9414 +NGF -0.6824 0.07589 0.9417 +WDR37 0.2218 0.076 0.9417 +NPFFR1 0.6156 0.07579 0.9417 +GIPC3 -0.696 0.07581 0.9417 +ERBB4 0.5386 0.07567 0.9417 +GHR -0.6939 0.07599 0.9417 +VWDE -0.6838 0.07595 0.9417 +RPS4X -0.5797 0.0761 0.9423 +CDK2AP2 -0.3551 0.07631 0.9432 +LOC146336 0.693 0.07658 0.9432 +UBE2C -0.6278 0.07624 0.9432 +C22orf39 0.2448 0.07654 0.9432 +MFSD7 -0.6817 0.07645 0.9432 +CANX -0.2312 0.07664 0.9432 +VIPR2 0.6908 0.07663 0.9432 +PPP1R3B -0.5682 0.07643 0.9432 +TMEM229B 0.5479 0.0767 0.9433 +PCDH17 0.2916 0.07683 0.9434 +HOXA10 -0.6931 0.0768 0.9434 +SYT12 0.5719 0.077 0.9434 +FLJ44054 -0.6519 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 0.9479 +LOC653653 -0.4477 0.0791 0.9479 +ZNF512 0.2908 0.07935 0.9479 +SNHG11 0.2322 0.07955 0.9479 +CDH22 0.6411 0.07954 0.9479 +PTK7 -0.5221 0.07951 0.9479 +ZP3 -0.6679 0.07931 0.9479 +TMEM53 0.3107 0.08059 0.9479 +LRRC7 0.3219 0.08033 0.9479 +GSTM2 -0.5028 0.08061 0.9479 +CASP7 -0.4341 0.08068 0.9479 +PPFIBP2 -0.6376 0.08024 0.9479 +THAP2 0.2884 0.07976 0.9479 +HSP90AB4P -0.6784 0.08068 0.9479 +DET1 0.2051 0.08049 0.9479 +CYLD 0.319 0.08012 0.9479 +BCL3 -0.6233 0.0806 0.9479 +VWC2L 0.6372 0.07974 0.9479 +RNF25 0.1676 0.08019 0.9479 +CNTN4 0.504 0.07976 0.9479 +CISH -0.5241 0.08075 0.9479 +HADH -0.4319 0.08056 0.9479 +PCDHB11 0.4955 0.07996 0.9479 +GSR -0.1539 0.08022 0.9479 +GAS1 -0.6786 0.08036 0.9479 +RALGPS1 0.3386 0.08055 0.9479 +ASS1 -0.5933 0.07979 0.9479 +MAGT1 -0.483 0.08078 0.9479 +FOXRED1 0.2663 0.08087 0.9484 +APOBEC3F -0.6398 0.08099 0.9486 +PNMA6C 0.6833 0.08101 0.9486 +NYNRIN -0.5606 0.08159 0.9534 +PAFAH1B1 0.2687 0.08149 0.9534 +HLA-DPB1 -0.6257 0.08158 0.9534 +ACADL -0.6423 0.08166 0.9535 +TMCO4 -0.68 0.08216 0.9575 +STX12 0.2526 0.08372 0.9575 +LPPR5 0.4957 0.08319 0.9575 +SLC16A1 -0.3904 0.08384 0.9575 +HIST2H2AC -0.6177 0.08331 0.9575 +UNC5B -0.655 0.08316 0.9575 +DLG2 0.4321 0.08343 0.9575 +EPS8 -0.5223 0.0829 0.9575 +TMED10 -0.2748 0.08272 0.9575 +ZNF668 0.2764 0.08363 0.9575 +CDH5 -0.6796 0.08264 0.9575 +SERPINF2 -0.6734 0.08263 0.9575 +CCL2 -0.6794 0.08289 0.9575 +NSF 0.2745 0.08307 0.9575 +TBX2 -0.5658 0.0821 0.9575 +NANP -0.3152 0.08238 0.9575 +LAMA5 -0.4893 0.08354 0.9575 +APOL1 -0.6811 0.08247 0.9575 +RPL14 -0.537 0.08355 0.9575 +TXNRD3 -0.5488 0.08316 0.9575 +PEX5L 0.623 0.08268 0.9575 +LOC152217 0.4514 0.08238 0.9575 +TMEM171 -0.6135 0.08386 0.9575 +LRRC1 -0.3878 0.08257 0.9575 +SIM1 0.6275 0.0826 0.9575 +BVES -0.249 0.08263 0.9575 +LINC00242 0.5716 0.08302 0.9575 +PHF14 0.1599 0.08393 0.9575 +PLOD3 -0.4068 0.08346 0.9575 +XKR5 -0.6356 0.08384 0.9575 +RHOBTB2 0.4079 0.08357 0.9575 +ANXA1 -0.6786 0.08292 0.9575 +ATP2B3 0.5396 0.0839 0.9575 +SMAP2 0.2954 0.08422 0.9598 +MELK -0.5682 0.08424 0.9598 +IFI16 -0.6473 0.0848 0.9611 +LRRC52 0.6609 0.08565 0.9611 +HHAT -0.4914 0.08442 0.9611 +INPPL1 -0.3374 0.08545 0.9611 +TUBA1B -0.2308 0.08554 0.9611 +AACS -0.4244 0.08516 0.9611 +IGDCC4 -0.6063 0.08495 0.9611 +CD276 -0.2418 0.08544 0.9611 +ACAN -0.675 0.08512 0.9611 +LINC00526 0.4174 0.08504 0.9611 +ZNF675 0.2529 0.08507 0.9611 +IRF2BP1 0.189 0.08564 0.9611 +NEU4 0.6273 0.0854 0.9611 +CXADR 0.2793 0.08566 0.9611 +PDCD6IP -0.3005 0.08529 0.9611 +CHSY3 -0.6706 0.08494 0.9611 +PPP1R10 0.4539 0.08556 0.9611 +AMPH 0.4514 0.08561 0.9611 +MEGF9 0.3088 0.08556 0.9611 +MIR181A2HG 0.4623 0.0857 0.9611 +RPL7A -0.4194 0.08505 0.9611 +KIF4A -0.4928 0.08548 0.9611 +MORF4L2 -0.4217 0.0847 0.9611 +CORO1B -0.275 0.08577 0.9611 +IL34 -0.6733 0.08602 0.9627 +WNT5A -0.604 0.08596 0.9627 +PABPC3 -0.4561 0.08631 0.9632 +MCF2L 0.4215 0.08624 0.9632 +SAMD14 0.2885 0.08656 0.9632 +ZFP28 0.6693 0.08651 0.9632 +ZNF300 0.6722 0.08654 0.9632 +GTF2E2 -0.3225 0.0862 0.9632 +FNBP1 -0.3116 0.08656 0.9632 +PTGDS -0.6437 0.08661 0.9632 +ARSE -0.6553 0.08666 0.9632 +TMSB15B -0.449 0.08644 0.9632 +ROBO3 0.6583 0.08676 0.9637 +PPP1R26 0.2834 0.08692 0.9649 +SLC25A45 -0.6618 0.08698 0.9649 +ZSCAN2 0.2606 0.08722 0.9659 +WDR73 0.2182 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