{ "key": "Agliassa2018a", "citation": "Agliassa, Narayana, Bertea, Rodgers & Maffei (2018), Bioelectromagnetics 39(5):361-374", "doi": "10.1002/bem.22123", "pmcid": "PMC6032911", "provenance_class": "published_results", "data_availability_verbatim": "no Data Availability Statement is present in the article; the quantitative data appear only as main-text tables", "organism": "Arabidopsis thaliana", "field_regime": "near-null magnetic field against the local geomagnetic field, in a triaxial Helmholtz coil system", "source_table": null, "loci_in_table": 26, "qbo_loci_covered": [ "AT1G01060", "AT1G22770", "AT2G45660", "AT2G46830", "AT4G25420", "AT5G10140", "AT5G61380" ], "cells_parsed": 196, "cells_blank": 0, "rows_without_locus": 0, "tissues": [ "leaves", "floral meristem" ], "figures": [ { "id": "QBM-10", "study": "Agliassa, Narayana, Bertea, Rodgers & Maffei", "tissue": "leaves", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-10__Agliassa-Narayana-Bertea-Rodgers-Maffei__leaves.svg", "timepoints": [ "17", "19", "21", "22", "23", "28" ], "nodes_with_data": 3, "fraction_covered": 0.4286, "vmax": 2.3923, "nodes_reversing_direction": [ "FLOWERING_REGULATORS", "GA_SIGNALLING" ], "nodes_with_heatmap": [ "CIRCADIAN_CLOCK" ], "nodes_with_diverging_loci": [ "CIRCADIAN_CLOCK" ], "provenance": "Values are the authors' published results from Agliassa, Narayana, Bertea, Rodgers & Maffei (2018), Bioelectromagnetics 39(5):361-374 (doi:10.1002/bem.22123), not a reanalysis: NNMF-grown plants relative to GMF controls at the equivalent timepoint. No raw data was deposited \u2014 the Data Availability Statement reads \u201cno Data Availability Statement is present in the article; the quantitative data appear only as main-text tables\u201d. Reported as log2 fold change; values are signed fold change \u2014 never reported strictly between -1 and +1 \u2014 so a negative number is a reciprocal, not a log. leaves, 6 timepoints (17, 19, 21, 22, 23, 28). 3 of 7 identifier-bearing nodes received a series (43%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. 1 node(s) have loci that disagree in direction at the same timepoint (CIRCADIAN_CLOCK), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 2 node(s) reverse direction during the course (GA_SIGNALLING, FLOWERING_REGULATORS), which no single-contrast overlay can show.", "dropped_edge_labels": [ "SINGLET_TRIPLET->CIRCADIAN_CLOCK: 'CRY is a clock input'" ], "low_coverage_published": false, "per_node": [ { "node_id": "CIRCADIAN_CLOCK", "qbo": "QBO:CIRCADIAN_CLOCK", "loci": [ "AT2G46830", "AT1G01060", "AT5G61380", "AT1G22770" ], "timepoints": [ "17", "19", "21", "22", "23", "28" ], "log2": [ -2.3923, -0.7908, -0.4751, -0.8237, -1.5558, -1.0072 ], "sd": [ 0.1248, 0.1483, 0.1132, 0.5465, 0.0694, 0.0897 ], "peak": -2.3923, "peak_timepoint": "17", "reverses_direction": false, "evidence_tier": "T3", "per_locus": { "AT2G46830": [ -2.3923, -0.6508, -0.0286, -0.7225, -1.5558, -0.8237 ], "AT1G01060": [ -1.541, -0.7908, -0.3561, -0.8237, -0.0566, -1.0072 ], "AT5G61380": [ -1.111, -0.6229, -0.4751, -0.1763, -0.2987, -0.1763 ], "AT1G22770": [ 0.0566, 0.0976, 0.0144, -0.4005, -0.0566, 0.5945 ] }, "loci_diverge": true }, { "node_id": "GA_SIGNALLING", "qbo": "QBO:GA_SIGNALLING", "loci": [ "AT4G25420" ], "timepoints": [ "17", "19", "21", "22", "23", "28" ], "log2": [ -1.6369, -1.281, -0.3103, -1.1953, 0.2869, -0.263 ], "sd": [ 0.1299, 0.2137, 0.2443, 0.0567, 0.3193, 0.1443 ], "peak": -1.6369, "peak_timepoint": "17", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT4G25420": [ -1.6369, -1.281, -0.3103, -1.1953, 0.2869, -0.263 ] }, "loci_diverge": false }, { "node_id": "FLOWERING_REGULATORS", "qbo": "QBO:FLOWERING_REGULATORS", "loci": [ "AT5G10140" ], "timepoints": [ "17", "19", "21", "22", "23", "28" ], "log2": [ 0.9855, -0.1635, -0.1375, -0.8074, -1.1506, -1.9298 ], "sd": [ 0.1239, 0.0386, 0.1443, 0.0907, 0.182, 0.0303 ], "peak": -1.9298, "peak_timepoint": "28", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT5G10140": [ 0.9855, -0.1635, -0.1375, -0.8074, -1.1506, -1.9298 ] }, "loci_diverge": false } ] }, { "id": "QBM-10", "study": "Agliassa, Narayana, Bertea, Rodgers & Maffei", "tissue": "floral meristem", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-10__Agliassa-Narayana-Bertea-Rodgers-Maffei__floral-meristem.svg", "timepoints": [ "21", "22", "23", "28", "30" ], "nodes_with_data": 2, "fraction_covered": 0.2857, "vmax": 3.847, "nodes_reversing_direction": [ "FLOWERING_REGULATORS", "GA_SIGNALLING" ], "nodes_with_heatmap": [ "FLOWERING_REGULATORS" ], "nodes_with_diverging_loci": [ "FLOWERING_REGULATORS" ], "provenance": "Values are the authors' published results from Agliassa, Narayana, Bertea, Rodgers & Maffei (2018), Bioelectromagnetics 39(5):361-374 (doi:10.1002/bem.22123), not a reanalysis: NNMF-grown plants relative to GMF controls at the equivalent timepoint. No raw data was deposited \u2014 the Data Availability Statement reads \u201cno Data Availability Statement is present in the article; the quantitative data appear only as main-text tables\u201d. Reported as log2 fold change; values are signed fold change \u2014 never reported strictly between -1 and +1 \u2014 so a negative number is a reciprocal, not a log. floral meristem, 5 timepoints (21, 22, 23, 28, 30). 2 of 7 identifier-bearing nodes received a series (29%); 4 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. 1 node(s) have loci that disagree in direction at the same timepoint (FLOWERING_REGULATORS), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 2 node(s) reverse direction during the course (GA_SIGNALLING, FLOWERING_REGULATORS), which no single-contrast overlay can show.", "dropped_edge_labels": [], "low_coverage_published": false, "per_node": [ { "node_id": "GA_SIGNALLING", "qbo": "QBO:GA_SIGNALLING", "loci": [ "AT4G25420" ], "timepoints": [ "21", "22", "23", "28", "30" ], "log2": [ -0.8718, -0.9411, -0.4751, 0.0566, 0.0426 ], "sd": [ 0.1656, 0.1879, 0.2387, 0.111, 0.4622 ], "peak": -0.9411, "peak_timepoint": "22", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT4G25420": [ -0.8718, -0.9411, -0.4751, 0.0566, 0.0426 ] }, "loci_diverge": false }, { "node_id": "FLOWERING_REGULATORS", "qbo": "QBO:FLOWERING_REGULATORS", "loci": [ "AT5G10140", "AT2G45660" ], "timepoints": [ "21", "22", "23", "28", "30" ], "log2": [ -2.3219, -3.847, -2.4699, -1.7137, 0.8074 ], "sd": [ 0.1102, 0.1707, 0.0753, 0.0384, 0.1484 ], "peak": -3.847, "peak_timepoint": "22", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT5G10140": [ -2.3219, -3.847, -2.4699, -1.7137, 0.8074 ], "AT2G45660": [ 0.5261, 0.757, -0.2016, -1.3951, -0.0566 ] }, "loci_diverge": true } ] }, { "id": "QBM-08", "study": "Agliassa, Narayana, Bertea, Rodgers & Maffei", "tissue": "leaves", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-08__Agliassa-Narayana-Bertea-Rodgers-Maffei__leaves.svg", "timepoints": [ "17", "19", "21", "22", "23", "28" ], "nodes_with_data": 2, "fraction_covered": 0.2222, "vmax": 2.3923, "nodes_reversing_direction": [ "GA_SIGNALLING" ], "nodes_with_heatmap": [ "CIRCADIAN_CLOCK" ], "nodes_with_diverging_loci": [ "CIRCADIAN_CLOCK" ], "provenance": "Values are the authors' published results from Agliassa, Narayana, Bertea, Rodgers & Maffei (2018), Bioelectromagnetics 39(5):361-374 (doi:10.1002/bem.22123), not a reanalysis: NNMF-grown plants relative to GMF controls at the equivalent timepoint. No raw data was deposited \u2014 the Data Availability Statement reads \u201cno Data Availability Statement is present in the article; the quantitative data appear only as main-text tables\u201d. Reported as log2 fold change; values are signed fold change \u2014 never reported strictly between -1 and +1 \u2014 so a negative number is a reciprocal, not a log. leaves, 6 timepoints (17, 19, 21, 22, 23, 28). 2 of 9 identifier-bearing nodes received a series (22%); 10 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. 1 node(s) have loci that disagree in direction at the same timepoint (CIRCADIAN_CLOCK), so their single trace is the aggregator choosing between genes that are doing different things \u2014 read those per locus, not as a node. 1 node(s) reverse direction during the course (GA_SIGNALLING), which no single-contrast overlay can show.", "dropped_edge_labels": [], "low_coverage_published": true, "per_node": [ { "node_id": "GA_SIGNALLING", "qbo": "QBO:GA_SIGNALLING", "loci": [ "AT4G25420" ], "timepoints": [ "17", "19", "21", "22", "23", "28" ], "log2": [ -1.6369, -1.281, -0.3103, -1.1953, 0.2869, -0.263 ], "sd": [ 0.1299, 0.2137, 0.2443, 0.0567, 0.3193, 0.1443 ], "peak": -1.6369, "peak_timepoint": "17", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT4G25420": [ -1.6369, -1.281, -0.3103, -1.1953, 0.2869, -0.263 ] }, "loci_diverge": false }, { "node_id": "CIRCADIAN_CLOCK", "qbo": "QBO:CIRCADIAN_CLOCK", "loci": [ "AT2G46830", "AT1G01060", "AT5G61380", "AT1G22770" ], "timepoints": [ "17", "19", "21", "22", "23", "28" ], "log2": [ -2.3923, -0.7908, -0.4751, -0.8237, -1.5558, -1.0072 ], "sd": [ 0.1248, 0.1483, 0.1132, 0.5465, 0.0694, 0.0897 ], "peak": -2.3923, "peak_timepoint": "17", "reverses_direction": false, "evidence_tier": "T3", "per_locus": { "AT2G46830": [ -2.3923, -0.6508, -0.0286, -0.7225, -1.5558, -0.8237 ], "AT1G01060": [ -1.541, -0.7908, -0.3561, -0.8237, -0.0566, -1.0072 ], "AT5G61380": [ -1.111, -0.6229, -0.4751, -0.1763, -0.2987, -0.1763 ], "AT1G22770": [ 0.0566, 0.0976, 0.0144, -0.4005, -0.0566, 0.5945 ] }, "loci_diverge": true } ] }, { "id": "QBM-08", "study": "Agliassa, Narayana, Bertea, Rodgers & Maffei", "tissue": "floral meristem", "organism": "Arabidopsis thaliana", "svg": "maps/svg/QBM-08__Agliassa-Narayana-Bertea-Rodgers-Maffei__floral-meristem.svg", "timepoints": [ "21", "22", "23", "28", "30" ], "nodes_with_data": 1, "fraction_covered": 0.1111, "vmax": 0.9411, "nodes_reversing_direction": [ "GA_SIGNALLING" ], "nodes_with_heatmap": [], "nodes_with_diverging_loci": [], "provenance": "Values are the authors' published results from Agliassa, Narayana, Bertea, Rodgers & Maffei (2018), Bioelectromagnetics 39(5):361-374 (doi:10.1002/bem.22123), not a reanalysis: NNMF-grown plants relative to GMF controls at the equivalent timepoint. No raw data was deposited \u2014 the Data Availability Statement reads \u201cno Data Availability Statement is present in the article; the quantitative data appear only as main-text tables\u201d. Reported as log2 fold change; values are signed fold change \u2014 never reported strictly between -1 and +1 \u2014 so a negative number is a reciprocal, not a log. floral meristem, 5 timepoints (21, 22, 23, 28, 30). 1 of 9 identifier-bearing nodes received a series (11%); 10 nodes carry no gene identifier and cannot. multi-locus nodes aggregated by extreme at each timepoint. 1 node(s) reverse direction during the course (GA_SIGNALLING), which no single-contrast overlay can show.", "dropped_edge_labels": [], "low_coverage_published": true, "per_node": [ { "node_id": "GA_SIGNALLING", "qbo": "QBO:GA_SIGNALLING", "loci": [ "AT4G25420" ], "timepoints": [ "21", "22", "23", "28", "30" ], "log2": [ -0.8718, -0.9411, -0.4751, 0.0566, 0.0426 ], "sd": [ 0.1656, 0.1879, 0.2387, 0.111, 0.4622 ], "peak": -0.9411, "peak_timepoint": "22", "reverses_direction": true, "evidence_tier": "T2", "per_locus": { "AT4G25420": [ -0.8718, -0.9411, -0.4751, 0.0566, 0.0426 ] }, "loci_diverge": false } ] } ] }