{"@id": "1", "ftpfilenames": "Genes_TPM_Matrix_GSEnnnnn_tpm_spk3.csv", "descr": "File contains gene model list with TPM average and stddev for GSE and BIN (co_prop_id).", "format": "TSV", "script_name": "geo_bi_spark_xfrm.py", "script_type": "python", "layout": "GSES_ID|GSE_ID|CO_PROP_ID|species_dbxref_id|Gene|avgTPM|stddevTPM|countTPM|minGSM_ID", "sublayout": "", "active": "1", "no_data_flag": "0" }, {"@id": "2", "ftpfilenames": "Genes_TPM_Matrix_GSEnnnnn_tpm_spk3de.csv", "descr": "File contains various stats based on Differential Expression analysis between experiment and control BIN.", "format": "TSV", "script_name": "geo_bi_spark_xfrm.py", "script_type": "python", "layout": "GSE|ctrl_srr|ctrl_bin|exp_srr|exp_bin|Gene|logFC|logCPM|LR|Pvalue|FDR|species_dbxref_id|GSES_ID|avgTPM|stddevTPM|ctrl_avgTPM|ctrl_stddevTPM", "sublayout": "", "active": "1", "no_data_flag": "0" } Genes_TPM_Matrix_GSE45786_tpm_spk3.csv GSES_ID GSE_ID CO_PROP_ID species_dbxref_id Gene avgTPM stddevTPM countTPM minGSM_ID 157 45786 1033 128 XL-9_2-gene33954 1.83 1 1115088 157 45786 1033 128 XL-9_2-gene24800 0.27 1 1115088 157 45786 1033 128 XL-9_2-gene37319 0.72 1 1115088 Genes_TPM_Matrix_GSE45786_tpm_spk3de.csv GSE ctrl_srr ctrl_bin exp_srr exp_bin Gene logFC logCPM LR Pvalue FDR species_dbxref_id GSES_ID avgTPM stddevTPM ctrl_avgTPM ctrl_stddevTPM 45786 SRR808992 1033.0 SRR808993 1032 XL-9_2-gene10320 -0.0587418857880732 7.649711009679071 0.0144258578950417 0.904397838452727 1.0 128 157 113.61 125.51 45786 SRR808992 1033.0 SRR808993 1032 XL-9_2-gene108 -0.39610084040906196 4.2559961941859905 0.575313499417317 0.448155164971442 1.0 128 157 8.79 12.31 Genes_TPM_Matrix_GSE45786_tpm_spk3.csv field_name example_data definition GSES_ID 157 surrogate key for GSE GSE_ID 45786 GSE number CO_PROP_ID 1033 bin for experiment species_dbxref_id 128 dbxref identifier for XL or XT species version Gene XL-9_2-gene33954 seq_id for gene model avgTPM 1.83 average TPM for experiment stddevTPM Stddev TPM for experiment countTPM 1 minGSM_ID 1115088 first GSM ID in bin [ { "field_name": "GSES_ID", "example_data": 157, "definition": "surrogate key for GSE\r" }, { "field_name": "GSE_ID", "example_data": 45786, "definition": "GSE number\r" }, { "field_name": "CO_PROP_ID", "example_data": 1033, "definition": "bin for experiment\r" }, { "field_name": "species_dbxref_id", "example_data": 128, "definition": "dbxref identifier for XL or XT species version\r" }, { "field_name": "Gene", "example_data": "XL-9_2-gene33954", "definition": "seq_id for gene model\r" }, { "field_name": "avgTPM", "example_data": 1.83, "definition": "average TPM for experiment\r" }, { "field_name": "stddevTPM", "example_data": null, "definition": "Stddev TPM for experiment\r" }, { "field_name": "countTPM", "example_data": 1, "definition": null }, { "field_name": "minGSM_ID", "example_data": 1115088, "definition": "first GSM ID in bin\r" }, { "field_name": null } ] Genes_TPM_Matrix_GSE45786_tpm_spk3de.csv field_name example_data definition GSE 45786 GSE number ctrl_srr SRR808992 ctrl_bin 1033 control bin exp_srr SRR808993 exp_bin 1032 experiment bin Gene XL-9_2-gene10320 seq_id for gene model logFC -0.058741886 log2 fold change (MLE): condition treated vs untreated logCPM 7.64971101 log Counts per million cpm LR 0.014425858 likelihood ratio Pvalue 0.904397838 differential expression P-value FDR 1 false detection rate fdr species_dbxref_id 128 dbxref identifier for XL or XT species version GSES_ID 157 surrogate key for GSE avgTPM 113.61 average TPM for experiment stddevTPM Stddev TPM for experiment ctrl_avgTPM 125.51 average TPM for control ctrl_stddevTPM Stddev TPM for control [ { "field_name": "GSE", "example_data": 45786, "definition": "GSE number\r" }, { "field_name": "ctrl_srr", "example_data": "SRR808992", "definition": null }, { "field_name": "ctrl_bin", "example_data": 1033, "definition": "control bin\r" }, { "field_name": "exp_srr", "example_data": "SRR808993", "definition": null }, { "field_name": "exp_bin", "example_data": 1032, "definition": "experiment bin\r" }, { "field_name": "Gene", "example_data": "XL-9_2-gene10320", "definition": "seq_id for gene model\r" }, { "field_name": "logFC", "example_data": -0.058741886, "definition": "log2 fold change (MLE): condition treated vs untreated \r" }, { "field_name": "logCPM", "example_data": 7.64971101, "definition": "log Counts per million cpm \r" }, { "field_name": "LR", "example_data": 0.014425858, "definition": "likelihood ratio \r" }, { "field_name": "Pvalue", "example_data": 0.904397838, "definition": "differential expression P-value \r" }, { "field_name": "FDR", "example_data": 1, "definition": "false detection rate fdr \r" }, { "field_name": "species_dbxref_id", "example_data": 128, "definition": "dbxref identifier for XL or XT species version\r" }, { "field_name": "GSES_ID", "example_data": 157, "definition": "surrogate key for GSE\r" }, { "field_name": "avgTPM", "example_data": 113.61, "definition": "average TPM for experiment\r" }, { "field_name": "stddevTPM", "example_data": null, "definition": "Stddev TPM for experiment\r" }, { "field_name": "ctrl_avgTPM", "example_data": 125.51, "definition": "average TPM for control\r" }, { "field_name": "ctrl_stddevTPM", "example_data": null, "definition": "Stddev TPM for control\r" }, { "field_name": null } ]