{ "accession": "OSD-782", "glds": "GLDS-679", "title": "Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation in Arabidopsis", "provenance_class": "genelab_processed", "organism": "Arabidopsis thaliana", "perturbation": { "kind": "ionising_radiation", "source": "cesium-137 gamma radiation", "doses_gy": [ 0.1, 1.0 ], "control": "non-irradiated", "note": "Ionising radiation is a different perturbation axis from magnetic field strength, not a point on it. QBO's field_regimes vocabulary is not used here and is not extended." }, "factors": [ "Ionizing Radiation", "Absorbed Radiation Dose", "Time of Sample Collection After Treatment" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "doses_gy": [ 0.1, 1.0 ], "contrasts": [ { "label": "(cesium-137 gamma radiation & 10 centigray & 1 hour)v(non-irradiated & 0 centigray & 1 hour)", "dose_gy": 0.1, "time": "1 hour", "hours": 1.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 10 centigray & 3 hour)v(non-irradiated & 0 centigray & 3 hour)", "dose_gy": 0.1, "time": "3 hour", "hours": 3.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 10 centigray & 24 hour)v(non-irradiated & 0 centigray & 24 hour)", "dose_gy": 0.1, "time": "24 hour", "hours": 24.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 10 centigray & 72 hour)v(non-irradiated & 0 centigray & 72 hour)", "dose_gy": 0.1, "time": "72 hour", "hours": 72.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 100 centigray & 1 hour)v(non-irradiated & 0 centigray & 1 hour)", "dose_gy": 1.0, "time": "1 hour", "hours": 1.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 100 centigray & 3 hour)v(non-irradiated & 0 centigray & 3 hour)", "dose_gy": 1.0, "time": "3 hour", "hours": 3.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 100 centigray & 24 hour)v(non-irradiated & 0 centigray & 24 hour)", "dose_gy": 1.0, "time": "24 hour", "hours": 24.0, "is_single_factor": false }, { "label": "(cesium-137 gamma radiation & 100 centigray & 72 hour)v(non-irradiated & 0 centigray & 72 hour)", "dose_gy": 1.0, "time": "72 hour", "hours": 72.0, "is_single_factor": false } ], "alpha": 0.05, "slice": { "cached": true, "output": "data/external/osd782_dose_contrasts.csv" }, "qbo_loci_measured": 123, "specificity": { "0.1 Gy": { "1 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.28959, "background_mean": 0.4226, "background_sd": 0.05657, "p_value": 0.9971, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "3 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.2409, "background_mean": 0.34849, "background_sd": 0.05753, "p_value": 0.9888, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "24 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.20417, "background_mean": 0.32512, "background_sd": 0.05646, "p_value": 0.9984, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "72 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.1815, "background_mean": 0.33456, "background_sd": 0.05078, "p_value": 1.0, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false } }, "1 Gy": { "1 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.19362, "background_mean": 0.37893, "background_sd": 0.05641, "p_value": 1.0, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "3 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.29872, "background_mean": 0.35666, "background_sd": 0.05546, "p_value": 0.86521, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "24 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.20918, "background_mean": 0.29701, "background_sd": 0.04908, "p_value": 0.9806, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "72 hour": { "n_selected_measured": 123, "n_background_loci": 23544, "observed_mean_abs_log2fc": 0.29266, "background_mean": 0.37862, "background_sd": 0.06436, "p_value": 0.92471, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false } } }, "maps": { "QBM-07": { "0.1 Gy": { "nodes_with_data": 8, "addressable": 8, "fraction": 1.0 }, "1 Gy": { "nodes_with_data": 8, "addressable": 8, "fraction": 1.0 } }, "QBM-01": { "0.1 Gy": { "nodes_with_data": 10, "addressable": 10, "fraction": 1.0 }, "1 Gy": { "nodes_with_data": 10, "addressable": 10, "fraction": 1.0 } }, "QBM-04": { "0.1 Gy": { "nodes_with_data": 10, "addressable": 10, "fraction": 1.0 }, "1 Gy": { "nodes_with_data": 10, "addressable": 10, "fraction": 1.0 } } }, "figures": [ { "id": "QBM-07", "study": "OSD-782 \u2014 0.1 Gy", "tissue": "0.1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-07__OSD-782-0-1-Gy__0-1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 8, "fraction_covered": 1.0, "vmax": 1.8937, "nodes_reversing_direction": [ "ASC_GSH_CYCLE", "CATALASE", "COMPLEX_I", "MITO_SUPEROXIDE", "PEROXIREDOXIN_TRX" ], "nodes_with_heatmap": [ "ASCORBATE_PEROXIDASE", "ASC_GSH_CYCLE", "CATALASE", "COMPLEX_I", "PLASTID_ROS", "SUPEROXIDE_DISMUTASES" ], "nodes_with_diverging_loci": [ "ASCORBATE_PEROXIDASE", "ASC_GSH_CYCLE", "CATALASE", "COMPLEX_I", "PLASTID_ROS", "SUPEROXIDE_DISMUTASES" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 0.1 Gy against non-irradiated controls at matched time. 0.1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 8 of 8 identifier-bearing nodes received a series (100%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 6 node(s) have loci that disagree in direction at the same timepoint (COMPLEX_I, PLASTID_ROS, SUPEROXIDE_DISMUTASES, ASCORBATE_PEROXIDASE\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 5 node(s) reverse direction during the course (COMPLEX_I, MITO_SUPEROXIDE, CATALASE, PEROXIREDOXIN_TRX\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [ "MITO_SUPEROXIDE->SUPEROXIDE_DISMUTASES: 'O2\u00b7\u2212 \u2192 H2O2'" ], "dose_gy": 0.1, "per_node": [ { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0392, 0.055, -0.1818, -0.1282 ], "peak": -0.1818, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "PLASTID_ROS", "qbo": "QBO:PLASTID_ROS", "loci": [ "AT4G25100", "AT2G28190" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.5871, -0.55, -0.4376, -0.4365 ], "peak": -0.5871, "peak_timepoint": "1 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T2" }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "loci": [ "AT3G10920" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0123, 0.039, -0.0797, -0.0507 ], "peak": -0.0797, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T2" }, { "node_id": "SUPEROXIDE_DISMUTASES", "qbo": "QBO:SUPEROXIDE_DISMUTASES", "loci": [ "AT1G08830", "AT2G28190", "AT3G10920", "AT4G25100" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.5871, -0.55, -0.4376, -0.4365 ], "peak": -0.5871, "peak_timepoint": "1 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T4" }, { "node_id": "ASCORBATE_PEROXIDASE", "qbo": "QBO:ASCORBATE_PEROXIDASE", "loci": [ "AT1G07890", "AT3G09640" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.2423, -1.8937, -0.2709, -0.8474 ], "peak": -1.8937, "peak_timepoint": "3 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T3" }, { "node_id": "CATALASE", "qbo": "QBO:CATALASE", "loci": [ "AT1G20630", "AT4G35090", "AT1G20620" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.2473, 0.2635, -0.2713, 0.6145 ], "peak": 0.6145, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "PEROXIREDOXIN_TRX", "qbo": "QBO:PEROXIREDOXIN_TRX", "loci": [ "AT3G06050" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0063, 0.0512, -0.12, -0.0594 ], "peak": -0.12, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "ASC_GSH_CYCLE", "qbo": "QBO:ASC_GSH_CYCLE", "loci": [ "AT3G24170", "AT1G19570", "AT3G52880" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.2712, 0.7967, 0.4394, 0.3075 ], "peak": 0.7967, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" } ] }, { "id": "QBM-01", "study": "OSD-782 \u2014 0.1 Gy", "tissue": "0.1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-01__OSD-782-0-1-Gy__0-1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 10, "fraction_covered": 1.0, "vmax": 2.1334, "nodes_reversing_direction": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I", "COMPLEX_II", "COMPLEX_I_FMN", "MITO_SUPEROXIDE", "RIESKE_FES" ], "nodes_with_heatmap": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I", "COMPLEX_II", "CYTOCHROME_C", "RIESKE_FES" ], "nodes_with_diverging_loci": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I", "COMPLEX_II", "RIESKE_FES" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 0.1 Gy against non-irradiated controls at matched time. 0.1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 10 of 10 identifier-bearing nodes received a series (100%); 7 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 6 node(s) have loci that disagree in direction at the same timepoint (COMPLEX_I, COMPLEX_II, ALT_NADH_DH, AOX\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 8 node(s) reverse direction during the course (COMPLEX_I, COMPLEX_I_FMN, COMPLEX_II, ALT_NADH_DH\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [], "dose_gy": 0.1, "per_node": [ { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0392, 0.055, -0.1818, -0.1282 ], "peak": -0.1818, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "COMPLEX_I_FMN", "qbo": "QBO:COMPLEX_I_FMN", "loci": [ "AT5G08530" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0392, 0.055, -0.1818, -0.0361 ], "peak": -0.1818, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "COMPLEX_II", "qbo": "QBO:COMPLEX_II", "loci": [ "AT5G66760", "AT3G27380", "AT5G40650", "AT5G09600", "AT2G46505" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1687, 0.22, 0.1878, -0.182 ], "peak": 0.22, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "ALT_NADH_DH", "qbo": "QBO:ALT_NADH_DH", "loci": [ "AT1G07180", "AT2G29990", "AT4G28220", "AT4G05020", "AT2G20800" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 1.4948, 0.5436, -0.9216, -0.9275 ], "peak": 1.4948, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T3" }, { "node_id": "AOX", "qbo": "QBO:AOX", "loci": [ "AT3G22370", "AT3G27620", "AT1G32350", "AT5G64210" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 2.1334, 1.9498, 1.7554, -0.8766 ], "peak": 2.1334, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T4" }, { "node_id": "RIESKE_FES", "qbo": "QBO:RIESKE_FES", "loci": [ "AT5G13430", "AT5G13440" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0589, -0.1101, -0.1149, -0.1931 ], "peak": -0.1931, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" }, { "node_id": "CYTOCHROME_C", "qbo": "QBO:CYTOCHROME_C", "loci": [ "AT1G22840", "AT4G10040" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0519, -0.0257, -0.2718, -0.2087 ], "peak": -0.2718, "peak_timepoint": "24 hour", "reverses_direction": false, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "loci": [ "AT3G10920" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0123, 0.039, -0.0797, -0.0507 ], "peak": -0.0797, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T2" }, { "node_id": "ACONITASE", "qbo": "QBO:ACONITASE", "loci": [ "AT4G35830", "AT4G26970", "AT2G05710" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.1062, 0.1324, -0.0819, 0.2201 ], "peak": 0.2201, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" }, { "node_id": "LIPOYL_SYNTHASE", "qbo": "QBO:LIPOYL_SYNTHASE", "loci": [ "AT2G20860" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0305, -0.005, -0.163, -0.1087 ], "peak": -0.163, "peak_timepoint": "24 hour", "reverses_direction": false, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" } ] }, { "id": "QBM-04", "study": "OSD-782 \u2014 0.1 Gy", "tissue": "0.1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-04__OSD-782-0-1-Gy__0-1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 10, "fraction_covered": 1.0, "vmax": 0.3692, "nodes_reversing_direction": [ "ATM3_EXPORT", "CIA_SYSTEM", "CNFU_HCF101", "FRATAXIN", "HSCB_GRXS15", "ISU1", "NFS1", "NFU_CARRIERS", "SUF_SYSTEM" ], "nodes_with_heatmap": [ "CIA_SYSTEM", "FES_CLIENTS", "HSCB_GRXS15", "NFU_CARRIERS", "SUF_SYSTEM" ], "nodes_with_diverging_loci": [ "CIA_SYSTEM", "FES_CLIENTS", "HSCB_GRXS15", "NFU_CARRIERS", "SUF_SYSTEM" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 0.1 Gy against non-irradiated controls at matched time. 0.1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 10 of 10 identifier-bearing nodes received a series (100%); 1 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 5 node(s) have loci that disagree in direction at the same timepoint (HSCB_GRXS15, NFU_CARRIERS, SUF_SYSTEM, CIA_SYSTEM\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 9 node(s) reverse direction during the course (NFS1, ISU1, FRATAXIN, HSCB_GRXS15\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [ "NFS1->ISU1: 'persulfide'", "FRATAXIN->ISU1: 'Fe donation'", "ISU1->HSCB_GRXS15: 'release'" ], "dose_gy": 0.1, "per_node": [ { "node_id": "NFS1", "qbo": "QBO:NFS1", "loci": [ "AT5G65720" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0585, -0.0008, -0.1344, -0.0511 ], "peak": -0.1344, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "ISU1", "qbo": "QBO:ISU1", "loci": [ "AT4G22220" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0499, 0.0482, -0.1069, -0.0089 ], "peak": -0.1069, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "FRATAXIN", "qbo": "QBO:FRATAXIN", "loci": [ "AT4G03240" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1578, -0.0353, 0.1301, -0.0651 ], "peak": 0.1578, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "HSCB_GRXS15", "qbo": "QBO:HSCB_GRXS15", "loci": [ "AT5G06410", "AT3G15660" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0751, 0.0965, -0.1187, -0.1538 ], "peak": -0.1538, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 1, "evidence_tier": "T3" }, { "node_id": "NFU_CARRIERS", "qbo": "QBO:NFU_CARRIERS", "loci": [ "AT3G20970", "AT1G51390" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.087, -0.1339, 0.1034, 0.0974 ], "peak": -0.1339, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 1, "evidence_tier": "T3" }, { "node_id": "ATM3_EXPORT", "qbo": "QBO:ATM3_EXPORT", "loci": [ "AT5G58270" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0366, 0.053, -0.1437, -0.1277 ], "peak": -0.1437, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "SUF_SYSTEM", "qbo": "QBO:SUF_SYSTEM", "loci": [ "AT1G08490", "AT4G26500" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.2402, 0.0907, -0.1175, -0.0485 ], "peak": -0.2402, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" }, { "node_id": "CNFU_HCF101", "qbo": "QBO:CNFU_HCF101", "loci": [ "AT3G24430" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0627, 0.0144, -0.2143, -0.0891 ], "peak": -0.2143, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "CIA_SYSTEM", "qbo": "QBO:CIA_SYSTEM", "loci": [ "AT5G50960", "AT4G16440", "AT2G26060", "AT1G68310", "AT5G48120" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.2437, 0.1514, -0.2299, -0.1949 ], "peak": 0.2437, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" }, { "node_id": "FES_CLIENTS", "qbo": "QBO:FES_CLIENTS", "loci": [ "AT4G35830", "AT5G66760", "AT5G13430", "AT4G03280", "AT1G10960", "AT2G20860", "AT2G21790" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.3051, -0.2591, -0.2572, -0.3692 ], "peak": -0.3692, "peak_timepoint": "72 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" } ] }, { "id": "QBM-07", "study": "OSD-782 \u2014 1 Gy", "tissue": "1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-07__OSD-782-1-Gy__1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 8, "fraction_covered": 1.0, "vmax": 1.8973, "nodes_reversing_direction": [ "ASCORBATE_PEROXIDASE", "ASC_GSH_CYCLE", "CATALASE", "MITO_SUPEROXIDE", "PEROXIREDOXIN_TRX", "PLASTID_ROS", "SUPEROXIDE_DISMUTASES" ], "nodes_with_heatmap": [ "ASCORBATE_PEROXIDASE", "ASC_GSH_CYCLE", "CATALASE", "COMPLEX_I", "PLASTID_ROS", "SUPEROXIDE_DISMUTASES" ], "nodes_with_diverging_loci": [ "ASC_GSH_CYCLE", "CATALASE", "COMPLEX_I", "PLASTID_ROS", "SUPEROXIDE_DISMUTASES" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 1 Gy against non-irradiated controls at matched time. 1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 8 of 8 identifier-bearing nodes received a series (100%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 5 node(s) have loci that disagree in direction at the same timepoint (COMPLEX_I, PLASTID_ROS, SUPEROXIDE_DISMUTASES, CATALASE\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 7 node(s) reverse direction during the course (PLASTID_ROS, MITO_SUPEROXIDE, SUPEROXIDE_DISMUTASES, ASCORBATE_PEROXIDASE\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [ "MITO_SUPEROXIDE->SUPEROXIDE_DISMUTASES: 'O2\u00b7\u2212 \u2192 H2O2'" ], "dose_gy": 1.0, "per_node": [ { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0335, -0.2636, -0.0556, -0.1516 ], "peak": -0.2636, "peak_timepoint": "3 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "PLASTID_ROS", "qbo": "QBO:PLASTID_ROS", "loci": [ "AT4G25100", "AT2G28190" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1047, -0.5556, -0.2087, -0.2582 ], "peak": -0.5556, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T2" }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "loci": [ "AT3G10920" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0115, -0.0742, -0.0469, -0.0202 ], "peak": -0.0742, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T2" }, { "node_id": "SUPEROXIDE_DISMUTASES", "qbo": "QBO:SUPEROXIDE_DISMUTASES", "loci": [ "AT1G08830", "AT2G28190", "AT3G10920", "AT4G25100" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1047, -0.5556, -0.2087, -0.2582 ], "peak": -0.5556, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T4" }, { "node_id": "ASCORBATE_PEROXIDASE", "qbo": "QBO:ASCORBATE_PEROXIDASE", "loci": [ "AT1G07890", "AT3G09640" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.4925, -1.7937, -0.2751, 1.8973 ], "peak": 1.8973, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "CATALASE", "qbo": "QBO:CATALASE", "loci": [ "AT1G20630", "AT4G35090", "AT1G20620" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.1997, -0.2058, 0.2931, 0.9061 ], "peak": 0.9061, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T3" }, { "node_id": "PEROXIREDOXIN_TRX", "qbo": "QBO:PEROXIREDOXIN_TRX", "loci": [ "AT3G06050" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0608, -0.1007, -0.035, 0.0337 ], "peak": -0.1007, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "ASC_GSH_CYCLE", "qbo": "QBO:ASC_GSH_CYCLE", "loci": [ "AT3G24170", "AT1G19570", "AT3G52880" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1696, 0.3373, -0.1262, 0.3435 ], "peak": 0.3435, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T3" } ] }, { "id": "QBM-01", "study": "OSD-782 \u2014 1 Gy", "tissue": "1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-01__OSD-782-1-Gy__1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 10, "fraction_covered": 1.0, "vmax": 3.9572, "nodes_reversing_direction": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I_FMN", "MITO_SUPEROXIDE", "RIESKE_FES" ], "nodes_with_heatmap": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I", "COMPLEX_II", "CYTOCHROME_C", "RIESKE_FES" ], "nodes_with_diverging_loci": [ "ACONITASE", "ALT_NADH_DH", "AOX", "COMPLEX_I", "COMPLEX_II", "CYTOCHROME_C", "RIESKE_FES" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 1 Gy against non-irradiated controls at matched time. 1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 10 of 10 identifier-bearing nodes received a series (100%); 7 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 7 node(s) have loci that disagree in direction at the same timepoint (COMPLEX_I, COMPLEX_II, ALT_NADH_DH, AOX\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 6 node(s) reverse direction during the course (COMPLEX_I_FMN, ALT_NADH_DH, AOX, RIESKE_FES\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [], "dose_gy": 1.0, "per_node": [ { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0335, -0.2636, -0.0556, -0.1516 ], "peak": -0.2636, "peak_timepoint": "3 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "COMPLEX_I_FMN", "qbo": "QBO:COMPLEX_I_FMN", "loci": [ "AT5G08530" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0263, -0.0858, -0.0556, -0.0342 ], "peak": -0.0858, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "COMPLEX_II", "qbo": "QBO:COMPLEX_II", "loci": [ "AT5G66760", "AT3G27380", "AT5G40650", "AT5G09600", "AT2G46505" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1565, 0.2244, 0.0713, 0.4806 ], "peak": 0.4806, "peak_timepoint": "72 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "ALT_NADH_DH", "qbo": "QBO:ALT_NADH_DH", "loci": [ "AT1G07180", "AT2G29990", "AT4G28220", "AT4G05020", "AT2G20800" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 1.0767, -1.6548, -1.6197, -1.0843 ], "peak": -1.6548, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "AOX", "qbo": "QBO:AOX", "loci": [ "AT3G22370", "AT3G27620", "AT1G32350", "AT5G64210" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 1.9218, 1.7079, -2.4339, 3.9572 ], "peak": 3.9572, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T4" }, { "node_id": "RIESKE_FES", "qbo": "QBO:RIESKE_FES", "loci": [ "AT5G13430", "AT5G13440" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0768, -0.1151, -0.0201, -0.1008 ], "peak": -0.1151, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "CYTOCHROME_C", "qbo": "QBO:CYTOCHROME_C", "loci": [ "AT1G22840", "AT4G10040" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.1294, -0.1303, -0.1804, -0.1264 ], "peak": -0.1804, "peak_timepoint": "24 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 1, "evidence_tier": "T3" }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "loci": [ "AT3G10920" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0115, -0.0742, -0.0469, -0.0202 ], "peak": -0.0742, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T2" }, { "node_id": "ACONITASE", "qbo": "QBO:ACONITASE", "loci": [ "AT4G35830", "AT4G26970", "AT2G05710" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.106, -0.0933, 0.0787, 0.1722 ], "peak": 0.1722, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "LIPOYL_SYNTHASE", "qbo": "QBO:LIPOYL_SYNTHASE", "loci": [ "AT2G20860" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0227, -0.196, -0.0061, -0.1093 ], "peak": -0.196, "peak_timepoint": "3 hour", "reverses_direction": false, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" } ] }, { "id": "QBM-04", "study": "OSD-782 \u2014 1 Gy", "tissue": "1 Gy", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-04__OSD-782-1-Gy__1-Gy.svg", "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "nodes_with_data": 10, "fraction_covered": 1.0, "vmax": 0.6098, "nodes_reversing_direction": [ "CIA_SYSTEM", "FRATAXIN", "HSCB_GRXS15", "ISU1", "NFS1", "NFU_CARRIERS" ], "nodes_with_heatmap": [ "CIA_SYSTEM", "FES_CLIENTS", "HSCB_GRXS15", "NFU_CARRIERS", "SUF_SYSTEM" ], "nodes_with_diverging_loci": [ "CIA_SYSTEM", "FES_CLIENTS", "HSCB_GRXS15", "NFU_CARRIERS", "SUF_SYSTEM" ], "provenance": "NASA OSDR OSD-782 / GLDS-679, GeneLab-processed differential expression. cesium-137 gamma radiation at 1 Gy against non-irradiated controls at matched time. 1 gy, 4 timepoints (1 hour, 3 hour, 24 hour, 72 hour). 10 of 10 identifier-bearing nodes received a series (100%); 1 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. GeneLab reports log2 fold change directly; no conversion applied. 5 node(s) have loci that disagree in direction at the same timepoint (HSCB_GRXS15, NFU_CARRIERS, SUF_SYSTEM, CIA_SYSTEM\u2026), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 6 node(s) reverse direction during the course (NFS1, ISU1, FRATAXIN, HSCB_GRXS15\u2026), which no single-contrast overlay can show.", "dropped_edge_labels": [ "NFS1->ISU1: 'persulfide'", "FRATAXIN->ISU1: 'Fe donation'", "ISU1->HSCB_GRXS15: 'release'" ], "dose_gy": 1.0, "per_node": [ { "node_id": "NFS1", "qbo": "QBO:NFS1", "loci": [ "AT5G65720" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.013, 0.0185, -0.0425, -0.0126 ], "peak": -0.0425, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "ISU1", "qbo": "QBO:ISU1", "loci": [ "AT4G22220" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.063, -0.0236, -0.0667, 0.015 ], "peak": -0.0667, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "FRATAXIN", "qbo": "QBO:FRATAXIN", "loci": [ "AT4G03240" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0752, 0.0449, -0.0327, -0.2047 ], "peak": -0.2047, "peak_timepoint": "72 hour", "reverses_direction": true, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "HSCB_GRXS15", "qbo": "QBO:HSCB_GRXS15", "loci": [ "AT5G06410", "AT3G15660" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.0739, 0.1081, -0.1777, 0.0213 ], "peak": -0.1777, "peak_timepoint": "24 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 2, "evidence_tier": "T3" }, { "node_id": "NFU_CARRIERS", "qbo": "QBO:NFU_CARRIERS", "loci": [ "AT3G20970", "AT1G51390" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1914, 0.0898, -0.0801, 0.033 ], "peak": 0.1914, "peak_timepoint": "1 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "ATM3_EXPORT", "qbo": "QBO:ATM3_EXPORT", "loci": [ "AT5G58270" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0444, -0.0585, -0.0631, -0.0763 ], "peak": -0.0763, "peak_timepoint": "72 hour", "reverses_direction": false, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T4" }, { "node_id": "SUF_SYSTEM", "qbo": "QBO:SUF_SYSTEM", "loci": [ "AT1G08490", "AT4G26500" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0336, -0.0743, -0.0569, -0.1754 ], "peak": -0.1754, "peak_timepoint": "72 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 1, "evidence_tier": "T3" }, { "node_id": "CNFU_HCF101", "qbo": "QBO:CNFU_HCF101", "loci": [ "AT3G24430" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.0741, -0.1079, -0.0909, -0.1491 ], "peak": -0.1491, "peak_timepoint": "72 hour", "reverses_direction": false, "loci_diverge": false, "diverging_timepoints": 0, "evidence_tier": "T3" }, { "node_id": "CIA_SYSTEM", "qbo": "QBO:CIA_SYSTEM", "loci": [ "AT5G50960", "AT4G16440", "AT2G26060", "AT1G68310", "AT5G48120" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ 0.1779, 0.305, -0.0898, -0.085 ], "peak": 0.305, "peak_timepoint": "3 hour", "reverses_direction": true, "loci_diverge": true, "diverging_timepoints": 3, "evidence_tier": "T3" }, { "node_id": "FES_CLIENTS", "qbo": "QBO:FES_CLIENTS", "loci": [ "AT4G35830", "AT5G66760", "AT5G13430", "AT4G03280", "AT1G10960", "AT2G20860", "AT2G21790" ], "timepoints": [ "1 hour", "3 hour", "24 hour", "72 hour" ], "log2": [ -0.1117, -0.6098, -0.1844, -0.4892 ], "peak": -0.6098, "peak_timepoint": "3 hour", "reverses_direction": false, "loci_diverge": true, "diverging_timepoints": 4, "evidence_tier": "T3" } ] } ], "related_work": "OSD-782 is the held-out validation set of the Plant Ionizing-Radiation Kinetic Landscape pipeline (Barker 2026), so this projection does not duplicate that analysis." }