{ "accession": "OSD-8", "title": "Gravitational and magnetic field variations synergize to cause subtle variations in the global transcriptional state of Arabidopsis in vitro callus cultures", "publication_doi": "10.1186/1471-2164-13-105", "geo_series": "GSE29787", "platform": "GPL9020", "provenance_class": "depositor_normalised", "organism": "Arabidopsis thaliana", "value_definition": "normalized log2 ratio representing test g /reference 1g", "field_regime": "strong static field", "primary_group": "MAG_1g", "groups": [ { "key": "MAG_1g", "label": "Magnet 1g* vs outside, 16.5 T", "test": "MAG 1g*", "reference": "1g control outside the magnet", "n_arrays": 3, "arrays": [ "GSM738246", "GSM738247", "GSM738248" ], "field_tesla": 16.5, "reference_field_tesla": 0.0, "gravity": "1g", "reference_gravity": "1g", "isolates_field": true, "isolates_gravity": false, "loci_with_values": 29327 }, { "key": "MAG_mg", "label": "Magnet simulated \u00b5g vs 1g outside", "test": "MAG mg*", "reference": "1g control outside the magnet", "n_arrays": 3, "arrays": [ "GSM738240", "GSM738241", "GSM738242" ], "field_tesla": 10.1, "reference_field_tesla": 0.0, "gravity": "\u00b5g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": false, "loci_with_values": 29327 }, { "key": "MAG_0.1g", "label": "Magnet 0.1g* vs 1g outside", "test": "MAG 0.1g*", "reference": "1g control outside the magnet", "n_arrays": 3, "arrays": [ "GSM738243", "GSM738244", "GSM738245" ], "field_tesla": 14.7, "reference_field_tesla": 0.0, "gravity": "0.1g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": false, "loci_with_values": 29327 }, { "key": "MAG_1.9g", "label": "Magnet 1.9g* vs 1g outside", "test": "MAG 1.9g*", "reference": "1g control outside the magnet", "n_arrays": 2, "arrays": [ "GSM738249", "GSM738250" ], "field_tesla": 14.7, "reference_field_tesla": 0.0, "gravity": "1.9g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": false, "loci_with_values": 29327 }, { "key": "MAG_2g", "label": "Magnet 2g* vs 1g outside", "test": "MAG 2g*", "reference": "1g control outside the magnet", "n_arrays": 3, "arrays": [ "GSM738251", "GSM738252", "GSM738253" ], "field_tesla": 10.1, "reference_field_tesla": 0.0, "gravity": "2g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": false, "loci_with_values": 29327 }, { "key": "RPM_mg", "label": "Random-positioning \u00b5g vs its 1g control (no magnet)", "test": "RPM mg*", "reference": "RPM 1g control", "n_arrays": 3, "arrays": [ "GSM738254", "GSM738255", "GSM738256" ], "field_tesla": 0.0, "reference_field_tesla": 0.0, "gravity": "\u00b5g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": true, "loci_with_values": 29327 }, { "key": "LDC_2g", "label": "Centrifuge 2g vs its 1g control (no magnet)", "test": "LDC 2g", "reference": "LDC 1g control", "n_arrays": 3, "arrays": [ "GSM738237", "GSM738238", "GSM738239" ], "field_tesla": 0.0, "reference_field_tesla": 0.0, "gravity": "2g", "reference_gravity": "1g", "isolates_field": false, "isolates_gravity": true, "loci_with_values": 29327 } ], "platform_join": { "platform": "GPL9020", "rows": 45220, "probes": 43803, "control_spots": 1417, "probes_without_agi": 4546, "probes_with_agi_from_accession_string": 38613, "probes_with_agi_only_from_gene_symbol": 646, "distinct_loci": 29327 }, "specificity": { "MAG_1g": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.16604, "background_mean": 0.17632, "background_sd": 0.01813, "p_value": 0.70543, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "MAG_mg": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.19329, "background_mean": 0.22374, "background_sd": 0.02308, "p_value": 0.91341, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "MAG_0.1g": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.19457, "background_mean": 0.21755, "background_sd": 0.02235, "p_value": 0.84632, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "MAG_1.9g": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.20732, "background_mean": 0.22451, "background_sd": 0.0261, "p_value": 0.73653, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "MAG_2g": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.14153, "background_mean": 0.14833, "background_sd": 0.01593, "p_value": 0.65293, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "RPM_mg": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.18367, "background_mean": 0.19841, "background_sd": 0.01861, "p_value": 0.78642, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false }, "LDC_2g": { "n_selected_measured": 125, "n_background_loci": 29202, "observed_mean_abs_log2fc": 0.19332, "background_mean": 0.20742, "background_sd": 0.02314, "p_value": 0.71933, "permutations": 10000, "seed": 20260924, "one_sided": "selected loci respond MORE than random loci", "significant_at_0.05": false } }, "maps": { "QBM-01": { "nodes_with_data": 10, "addressable": 10, "fraction": 1.0, "vmax": 0.5061, "nodes": [ { "node_id": "ACONITASE", "qbo": "QBO:ACONITASE", "evidence_tier": "T3", "loci": [ "AT4G35830", "AT4G26970", "AT2G05710" ], "by_group": { "MAG_1g": 0.4044, "MAG_mg": 0.5061, "MAG_0.1g": 0.3961, "MAG_1.9g": 0.3033, "MAG_2g": 0.3289, "RPM_mg": 0.0578, "LDC_2g": -0.2139 } }, { "node_id": "COMPLEX_I_FMN", "qbo": "QBO:COMPLEX_I_FMN", "evidence_tier": "T3", "loci": [ "AT5G08530" ], "by_group": { "MAG_1g": 0.32, "MAG_mg": 0.12, "MAG_0.1g": 0.0167, "MAG_1.9g": 0.275, "MAG_2g": 0.0667, "RPM_mg": 0.1233, "LDC_2g": -0.01 } }, { "node_id": "AOX", "qbo": "QBO:AOX", "evidence_tier": "T4", "loci": [ "AT3G22370", "AT3G22360", "AT3G27620", "AT1G32350", "AT5G64210" ], "by_group": { "MAG_1g": -0.1757, "MAG_mg": -0.1487, "MAG_0.1g": -0.1193, "MAG_1.9g": -0.3975, "MAG_2g": -0.1783, "RPM_mg": 0.115, "LDC_2g": -0.0937 } }, { "node_id": "LIPOYL_SYNTHASE", "qbo": "QBO:LIPOYL_SYNTHASE", "evidence_tier": "T3", "loci": [ "AT2G20860" ], "by_group": { "MAG_1g": 0.1733, "MAG_mg": 0.21, "MAG_0.1g": 0.1433, "MAG_1.9g": -0.145, "MAG_2g": 0.13, "RPM_mg": 0.3467, "LDC_2g": 0.1933 } }, { "node_id": "CYTOCHROME_C", "qbo": "QBO:CYTOCHROME_C", "evidence_tier": "T3", "loci": [ "AT1G22840", "AT4G10040" ], "by_group": { "MAG_1g": -0.1617, "MAG_mg": -0.0692, "MAG_0.1g": -0.0325, "MAG_1.9g": -0.195, "MAG_2g": -0.13, "RPM_mg": 0.0683, "LDC_2g": 0.1725 } }, { "node_id": "RIESKE_FES", "qbo": "QBO:RIESKE_FES", "evidence_tier": "T3", "loci": [ "AT5G13430", "AT5G13440" ], "by_group": { "MAG_1g": 0.0483, "MAG_mg": -0.0, "MAG_0.1g": -0.0225, "MAG_1.9g": -0.0275, "MAG_2g": 0.0333, "RPM_mg": 0.0017, "LDC_2g": 0.0167 } }, { "node_id": "COMPLEX_II", "qbo": "QBO:COMPLEX_II", "evidence_tier": "T3", "loci": [ "AT5G66760", "AT3G27380", "AT5G40650", "AT5G09600", "AT2G46505" ], "by_group": { "MAG_1g": -0.0367, "MAG_mg": 0.0233, "MAG_0.1g": 0.0203, "MAG_1.9g": 0.111, "MAG_2g": -0.0327, "RPM_mg": -0.053, "LDC_2g": -0.1047 } }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "evidence_tier": "T2", "loci": [ "AT3G10920" ], "by_group": { "MAG_1g": 0.0217, "MAG_mg": 0.0667, "MAG_0.1g": 0.0333, "MAG_1.9g": 0.17, "MAG_2g": -0.1733, "RPM_mg": 0.0383, "LDC_2g": -0.0383 } }, { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "evidence_tier": "T3", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "by_group": { "MAG_1g": -0.0137, "MAG_mg": -0.0667, "MAG_0.1g": -0.0758, "MAG_1.9g": 0.0406, "MAG_2g": -0.1042, "RPM_mg": -0.0158, "LDC_2g": -0.0429 } }, { "node_id": "ALT_NADH_DH", "qbo": "QBO:ALT_NADH_DH", "evidence_tier": "T3", "loci": [ "AT1G07180", "AT2G29990", "AT4G28220", "AT4G05020", "AT2G20800" ], "by_group": { "MAG_1g": -0.0057, "MAG_mg": 0.0463, "MAG_0.1g": 0.16, "MAG_1.9g": -0.103, "MAG_2g": -0.0987, "RPM_mg": 0.0257, "LDC_2g": -0.065 } } ] }, "QBM-03": { "nodes_with_data": 4, "addressable": 4, "fraction": 1.0, "vmax": 0.49, "nodes": [ { "node_id": "CRY1", "qbo": "QBO:CRY1", "evidence_tier": "T1", "loci": [ "AT4G08920" ], "by_group": { "MAG_1g": 0.255, "MAG_mg": 0.1533, "MAG_0.1g": 0.245, "MAG_1.9g": -0.0175, "MAG_2g": 0.205, "RPM_mg": 0.0917, "LDC_2g": 0.49 } }, { "node_id": "TRP_TRIAD", "qbo": "QBO:TRP_TRIAD", "evidence_tier": "T2", "loci": [ "AT4G08920", "AT1G04400" ], "by_group": { "MAG_1g": 0.1442, "MAG_mg": 0.1175, "MAG_0.1g": 0.1892, "MAG_1.9g": -0.0163, "MAG_2g": 0.0842, "RPM_mg": 0.1675, "LDC_2g": 0.2725 } }, { "node_id": "PHYB", "qbo": "QBO:PHYB", "evidence_tier": "T4", "loci": [ "AT2G18790" ], "by_group": { "MAG_1g": -0.1067, "MAG_mg": 0.0233, "MAG_0.1g": -0.1133, "MAG_1.9g": -0.045, "MAG_2g": 0.0433, "RPM_mg": -0.06, "LDC_2g": -0.0233 } }, { "node_id": "CRY2", "qbo": "QBO:CRY2", "evidence_tier": "T2", "loci": [ "AT1G04400" ], "by_group": { "MAG_1g": 0.0333, "MAG_mg": 0.0817, "MAG_0.1g": 0.1333, "MAG_1.9g": -0.015, "MAG_2g": -0.0367, "RPM_mg": 0.2433, "LDC_2g": 0.055 } } ] }, "QBM-07": { "nodes_with_data": 8, "addressable": 8, "fraction": 1.0, "vmax": 0.565, "nodes": [ { "node_id": "PLASTID_ROS", "qbo": "QBO:PLASTID_ROS", "evidence_tier": "T2", "loci": [ "AT4G25100", "AT2G28190" ], "by_group": { "MAG_1g": 0.1817, "MAG_mg": 0.2317, "MAG_0.1g": 0.245, "MAG_1.9g": 0.0338, "MAG_2g": 0.0558, "RPM_mg": 0.1, "LDC_2g": 0.2033 } }, { "node_id": "CATALASE", "qbo": "QBO:CATALASE", "evidence_tier": "T3", "loci": [ "AT1G20630", "AT4G35090", "AT1G20620" ], "by_group": { "MAG_1g": -0.0989, "MAG_mg": -0.0522, "MAG_0.1g": -0.0489, "MAG_1.9g": 0.0367, "MAG_2g": -0.0444, "RPM_mg": -0.0689, "LDC_2g": -0.13 } }, { "node_id": "SUPEROXIDE_DISMUTASES", "qbo": "QBO:SUPEROXIDE_DISMUTASES", "evidence_tier": "T4", "loci": [ "AT1G08830", "AT2G28190", "AT3G10920", "AT4G25100" ], "by_group": { "MAG_1g": 0.0967, "MAG_mg": 0.1425, "MAG_0.1g": 0.1579, "MAG_1.9g": 0.0819, "MAG_2g": -0.035, "RPM_mg": 0.0675, "LDC_2g": 0.07 } }, { "node_id": "PEROXIREDOXIN_TRX", "qbo": "QBO:PEROXIREDOXIN_TRX", "evidence_tier": "T4", "loci": [ "AT3G06050" ], "by_group": { "MAG_1g": -0.0717, "MAG_mg": 0.09, "MAG_0.1g": -0.0183, "MAG_1.9g": 0.0675, "MAG_2g": 0.0117, "RPM_mg": 0.0083, "LDC_2g": -0.02 } }, { "node_id": "ASC_GSH_CYCLE", "qbo": "QBO:ASC_GSH_CYCLE", "evidence_tier": "T3", "loci": [ "AT3G24170", "AT1G19570", "AT3G52880" ], "by_group": { "MAG_1g": 0.0467, "MAG_mg": -0.0522, "MAG_0.1g": -0.0444, "MAG_1.9g": 0.0933, "MAG_2g": 0.0856, "RPM_mg": -0.0722, "LDC_2g": -0.0317 } }, { "node_id": "ASCORBATE_PEROXIDASE", "qbo": "QBO:ASCORBATE_PEROXIDASE", "evidence_tier": "T3", "loci": [ "AT1G07890", "AT3G09640" ], "by_group": { "MAG_1g": 0.0267, "MAG_mg": 0.0167, "MAG_0.1g": -0.22, "MAG_1.9g": 0.565, "MAG_2g": 0.0367, "RPM_mg": 0.1617, "LDC_2g": -0.2417 } }, { "node_id": "MITO_SUPEROXIDE", "qbo": "QBO:MITO_SUPEROXIDE", "evidence_tier": "T2", "loci": [ "AT3G10920" ], "by_group": { "MAG_1g": 0.0217, "MAG_mg": 0.0667, "MAG_0.1g": 0.0333, "MAG_1.9g": 0.17, "MAG_2g": -0.1733, "RPM_mg": 0.0383, "LDC_2g": -0.0383 } }, { "node_id": "COMPLEX_I", "qbo": "QBO:COMPLEX_I", "evidence_tier": "T3", "loci": [ "AT5G37510", "AT5G08530", "AT4G02580", "AT5G11770" ], "by_group": { "MAG_1g": -0.0137, "MAG_mg": -0.0667, "MAG_0.1g": -0.0758, "MAG_1.9g": 0.0406, "MAG_2g": -0.1042, "RPM_mg": -0.0158, "LDC_2g": -0.0429 } } ] }, "QBM-09": { "nodes_with_data": 9, "addressable": 9, "fraction": 1.0, "vmax": 0.5875, "nodes": [ { "node_id": "CYSTEINE_SYNTHESIS", "qbo": "QBO:CYSTEINE_SYNTHESIS", "evidence_tier": "T4", "loci": [ "AT1G55920", "AT4G14880" ], "by_group": { "MAG_1g": 0.23, "MAG_mg": 0.5283, "MAG_0.1g": 0.3733, "MAG_1.9g": 0.5875, "MAG_2g": 0.4417, "RPM_mg": -0.1583, "LDC_2g": 0.2517 } }, { "node_id": "NFS1", "qbo": "QBO:NFS1", "evidence_tier": "T4", "loci": [ "AT5G65720" ], "by_group": { "MAG_1g": 0.2233, "MAG_mg": 0.145, "MAG_0.1g": 0.215, "MAG_1.9g": -0.0925, "MAG_2g": 0.125, "RPM_mg": 0.2533, "LDC_2g": 0.2733 } }, { "node_id": "ISU1", "qbo": "QBO:ISU1", "evidence_tier": "T3", "loci": [ "AT4G22220" ], "by_group": { "MAG_1g": 0.1533, "MAG_mg": 0.15, "MAG_0.1g": 0.18, "MAG_1.9g": 0.045, "MAG_2g": 0.0933, "RPM_mg": 0.07, "LDC_2g": 0.06 } }, { "node_id": "SUF_SYSTEM", "qbo": "QBO:SUF_SYSTEM", "evidence_tier": "T3", "loci": [ "AT1G08490", "AT4G26500" ], "by_group": { "MAG_1g": -0.1417, "MAG_mg": -0.2933, "MAG_0.1g": -0.1683, "MAG_1.9g": -0.1725, "MAG_2g": -0.035, "RPM_mg": -0.02, "LDC_2g": 0.3433 } }, { "node_id": "FE_UPTAKE", "qbo": "QBO:FE_UPTAKE", "evidence_tier": "T2", "loci": [ "AT1G01580", "AT4G19690", "AT2G28160", "AT3G56970", "AT3G56980", "AT1G23020" ], "by_group": { "MAG_1g": 0.0739, "MAG_mg": -0.0328, "MAG_0.1g": -0.0461, "MAG_1.9g": 0.1092, "MAG_2g": 0.0333, "RPM_mg": -0.0364, "LDC_2g": -0.0503 } }, { "node_id": "FES_CLIENTS", "qbo": "QBO:FES_CLIENTS", "evidence_tier": "T3", "loci": [ "AT4G35830", "AT5G66760", "AT5G13430", "AT4G03280", "AT1G10960", "AT2G20860", "AT2G21790" ], "by_group": { "MAG_1g": 0.0338, "MAG_mg": 0.034, "MAG_0.1g": -0.0048, "MAG_1.9g": -0.0064, "MAG_2g": 0.0195, "RPM_mg": -0.0262, "LDC_2g": 0.0462 } }, { "node_id": "FERREDOXIN", "qbo": "QBO:FERREDOXIN", "evidence_tier": "T2", "loci": [ "AT1G10960", "AT1G60950" ], "by_group": { "MAG_1g": -0.0267, "MAG_mg": -0.03, "MAG_0.1g": -0.0817, "MAG_1.9g": 0.0125, "MAG_2g": -0.0133, "RPM_mg": -0.01, "LDC_2g": -0.0167 } }, { "node_id": "S_ASSIMILATION", "qbo": "QBO:S_ASSIMILATION", "evidence_tier": "T2", "loci": [ "AT4G08620", "AT1G78000", "AT5G10180", "AT3G22890", "AT4G04610", "AT1G62180", "AT4G21990", "AT5G04590" ], "by_group": { "MAG_1g": 0.0169, "MAG_mg": 0.0933, "MAG_0.1g": 0.0881, "MAG_1.9g": 0.2519, "MAG_2g": 0.089, "RPM_mg": -0.1773, "LDC_2g": -0.3871 } }, { "node_id": "FE_STORAGE", "qbo": "QBO:FE_STORAGE", "evidence_tier": "T4", "loci": [ "AT5G01600", "AT2G40300", "AT1G56430", "AT2G23150", "AT5G67330", "AT3G12750" ], "by_group": { "MAG_1g": 0.0047, "MAG_mg": 0.0797, "MAG_0.1g": 0.1086, "MAG_1.9g": -0.0537, "MAG_2g": -0.0411, "RPM_mg": 0.1289, "LDC_2g": 0.2683 } } ] } }, "figures": [ { "id": "QBM-01", "study": "OSD-8", "contrast": "MAG_1g", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-01__OSD-8.svg", "nodes_with_data": 10, "fraction_covered": 1.0, "vmax": 0.5061, "provenance": "Data: OSD-8, contrast MAG_1g. organism Arabidopsis thaliana. 10 of 10 identifier-bearing nodes received a value (100%); 7 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by mean.", "dropped_edge_labels": [], "group": "MAG_1g", "group_label": "Magnet 1g* vs outside, 16.5 T" }, { "id": "QBM-03", "study": "OSD-8", "contrast": "MAG_1g", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-03__OSD-8.svg", "nodes_with_data": 4, "fraction_covered": 1.0, "vmax": 0.49, "provenance": "Data: OSD-8, contrast MAG_1g. organism Arabidopsis thaliana. 4 of 4 identifier-bearing nodes received a value (100%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by mean.", "dropped_edge_labels": [], "group": "MAG_1g", "group_label": "Magnet 1g* vs outside, 16.5 T" }, { "id": "QBM-07", "study": "OSD-8", "contrast": "MAG_1g", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-07__OSD-8.svg", "nodes_with_data": 8, "fraction_covered": 1.0, "vmax": 0.565, "provenance": "Data: OSD-8, contrast MAG_1g. organism Arabidopsis thaliana. 8 of 8 identifier-bearing nodes received a value (100%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by mean.", "dropped_edge_labels": [], "group": "MAG_1g", "group_label": "Magnet 1g* vs outside, 16.5 T" }, { "id": "QBM-09", "study": "OSD-8", "contrast": "MAG_1g", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-09__OSD-8.svg", "nodes_with_data": 9, "fraction_covered": 1.0, "vmax": 0.5875, "provenance": "Data: OSD-8, contrast MAG_1g. organism Arabidopsis thaliana. 9 of 9 identifier-bearing nodes received a value (100%); 1 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by mean.", "dropped_edge_labels": [], "group": "MAG_1g", "group_label": "Magnet 1g* vs outside, 16.5 T" } ] }