# research_records

record_id: DS057_R00187
dataset_id: DS057
record_json:
{"gene_id":"Ma06_g21680","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006950 | response to stress","all_three_pathway_count":"0","GO_annotation":"Biological Process: response to stress (GO:0006950);; ","Swiss_Prot_annotation":"Late embryogenesis abundant protein Lea5","NR_annotation":"PREDICTED: late embryogenesis abundant protein Lea5-D [Musa acuminata subsp. malaccensis]","recovery_log2fc":"-3.78054573766897","recovery_shrunk_log2fc":"-0.136027763506899","recovery_padj":"0.501127990905443","reciprocal_log2fc":"4.12835882199832","reciprocal_shrunk_log2fc":"2.77359541180854","reciprocal_padj":"3.8194884710911894e-11","exclude_pair_log2fc":"5.22209517396357","exclude_pair_shrunk_log2fc":"3.44499325018355","exclude_pair_padj":"1.42837592788115e-12","five_traceable_log2fc":"5.01925815036953","five_traceable_shrunk_log2fc":"3.50829250862916","five_traceable_padj":"8.92326676070768e-14","paper_counts_log2fc":"5.41014418354224","paper_counts_shrunk_log2fc":"3.59696168255793","paper_counts_padj":"7.75501059257051e-15","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma06_g21680 | 1 | 1 | RNA and ribosome biogenesis | GO:0006950 | response to stress | 0 | Biological Process: response to stress (GO:0006950);;  | Late embryogenesis abundant protein Lea5 | PREDICTED: late embryogenesis abundant protein Lea5-D [Musa acuminata subsp. malaccensis] | -3.78054573766897 | -0.136027763506899 | 0.501127990905443 | 4.12835882199832 | 2.77359541180854 | 3.8194884710911894e-11 | 5.22209517396357 | 3.44499325018355 | 1.42837592788115e-12 | 5.01925815036953 | 3.50829250862916 | 8.92326676070768e-14 | 5.41014418354224 | 3.59696168255793 | 7.75501059257051e-15 | True | True


record_id: DS057_R00188
dataset_id: DS057
record_json:
{"gene_id":"Ma07_g04010","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0043169 | cation binding","all_three_pathway_count":"0","GO_annotation":"Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Cellular Component: integral component of membrane (GO:0016021);; Molecular Function: metal ion binding (GO:0046872);; ","Swiss_Prot_annotation":"Probable protein phosphatase 2C 60","NR_annotation":"PREDICTED: probable protein phosphatase 2C 60 [Musa acuminata subsp. malaccensis] ","recovery_log2fc":"-1.058195519719","recovery_shrunk_log2fc":"-0.624971333745489","recovery_padj":"0.232201594329852","reciprocal_log2fc":"0.555227657692378","reciprocal_shrunk_log2fc":"0.539281949074097","reciprocal_padj":"0.0010610067326956","exclude_pair_log2fc":"0.501114958088879","exclude_pair_shrunk_log2fc":"0.466384253036708","exclude_pair_padj":"0.168644835311239","five_traceable_log2fc":"0.51374503720641","five_traceable_shrunk_log2fc":"0.499123472223507","five_traceable_padj":"0.0063737375627502","paper_counts_log2fc":"0.593135625391728","paper_counts_shrunk_log2fc":"0.586854261090291","paper_counts_padj":"1.34908862212291e-08","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma07_g04010 | 1 | 1 | RNA and ribosome biogenesis | GO:0043169 | cation binding | 0 | Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Cellular Component: integral component of membrane (GO:0016021);; Molecular Function: metal ion binding (GO:0046872);;  | Probable protein phosphatase 2C 60 | PREDICTED: probable protein phosphatase 2C 60 [Musa acuminata subsp. malaccensis]  | -1.058195519719 | -0.624971333745489 | 0.232201594329852 | 0.555227657692378 | 0.539281949074097 | 0.0010610067326956 | 0.501114958088879 | 0.466384253036708 | 0.168644835311239 | 0.51374503720641 | 0.499123472223507 | 0.0063737375627502 | 0.593135625391728 | 0.586854261090291 | 1.34908862212291e-08 | True | True


record_id: DS057_R00189
dataset_id: DS057
record_json:
{"gene_id":"Ma08_g21660","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006950 | response to stress","all_three_pathway_count":"0","GO_annotation":"Molecular Function: ATP binding (GO:0005524);; ","Swiss_Prot_annotation":"Heat shock cognate 70 kDa protein","NR_annotation":"PREDICTED: heat shock cognate 70 kDa protein 2-like [Musa acuminata subsp. malaccensis]","recovery_log2fc":"-0.673885484133982","recovery_shrunk_log2fc":"-0.478602757839681","recovery_padj":"0.380784001812531","reciprocal_log2fc":"1.05555600875147","reciprocal_shrunk_log2fc":"0.865731407579374","reciprocal_padj":"0.0334023535887926","exclude_pair_log2fc":"1.10331332756879","exclude_pair_shrunk_log2fc":"0.801604620427551","exclude_pair_padj":"0.18009642782729","five_traceable_log2fc":"1.02311906419933","five_traceable_shrunk_log2fc":"0.833939779542319","five_traceable_padj":"0.0648497274238391","paper_counts_log2fc":"1.05918202505318","paper_counts_shrunk_log2fc":"0.96785451985246","paper_counts_padj":"0.0011404171585749","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma08_g21660 | 1 | 1 | RNA and ribosome biogenesis | GO:0006950 | response to stress | 0 | Molecular Function: ATP binding (GO:0005524);;  | Heat shock cognate 70 kDa protein | PREDICTED: heat shock cognate 70 kDa protein 2-like [Musa acuminata subsp. malaccensis] | -0.673885484133982 | -0.478602757839681 | 0.380784001812531 | 1.05555600875147 | 0.865731407579374 | 0.0334023535887926 | 1.10331332756879 | 0.801604620427551 | 0.18009642782729 | 1.02311906419933 | 0.833939779542319 | 0.0648497274238391 | 1.05918202505318 | 0.96785451985246 | 0.0011404171585749 | True | True


record_id: DS057_R00190
dataset_id: DS057
record_json:
{"gene_id":"Ma08_g22950","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0043169 | cation binding","all_three_pathway_count":"0","GO_annotation":"Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);; ","Swiss_Prot_annotation":"Probable protein phosphatase 2C 2","NR_annotation":"PREDICTED: probable protein phosphatase 2C 47 [Musa acuminata subsp. malaccensis]","recovery_log2fc":"-3.10328743696332","recovery_shrunk_log2fc":"-0.201719879535143","recovery_padj":"","reciprocal_log2fc":"1.73677115788429","reciprocal_shrunk_log2fc":"1.44440078946401","reciprocal_padj":"5.49029919432729e-05","exclude_pair_log2fc":"1.42199845491062","exclude_pair_shrunk_log2fc":"1.05721669328102","exclude_pair_padj":"0.0478712414312717","five_traceable_log2fc":"1.57535120047268","five_traceable_shrunk_log2fc":"1.33469960697278","five_traceable_padj":"0.000478756201825","paper_counts_log2fc":"1.68210650019043","paper_counts_shrunk_log2fc":"1.54226221229048","paper_counts_padj":"3.31647592252216e-08","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma08_g22950 | 1 | 1 | RNA and ribosome biogenesis | GO:0043169 | cation binding | 0 | Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);;  | Probable protein phosphatase 2C 2 | PREDICTED: probable protein phosphatase 2C 47 [Musa acuminata subsp. malaccensis] | -3.10328743696332 | -0.201719879535143 | 1.73677115788429 | 1.44440078946401 | 5.49029919432729e-05 | 1.42199845491062 | 1.05721669328102 | 0.0478712414312717 | 1.57535120047268 | 1.33469960697278 | 0.000478756201825 | 1.68210650019043 | 1.54226221229048 | 3.31647592252216e-08 | True | True


record_id: DS057_R00191
dataset_id: DS057
record_json:
{"gene_id":"Ma08_g28260","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006353 | DNA-templated transcription termination","all_three_pathway_count":"0","GO_annotation":"--","Swiss_Prot_annotation":"SAP-like protein BP-73","NR_annotation":"PREDICTED: SAP-like protein BP-73 [Musa acuminata subsp. malaccensis]","recovery_log2fc":"0.478339761164731","recovery_shrunk_log2fc":"0.339628872443094","recovery_padj":"0.603415395179115","reciprocal_log2fc":"-0.32309389859166","reciprocal_shrunk_log2fc":"-0.296718604219112","reciprocal_padj":"0.387717102137916","exclude_pair_log2fc":"-0.467551326861477","exclude_pair_shrunk_log2fc":"-0.429810102927426","exclude_pair_padj":"0.261313623807845","five_traceable_log2fc":"-0.513401393899625","five_traceable_shrunk_log2fc":"-0.49403990184119","five_traceable_padj":"0.0218964653983011","paper_counts_log2fc":"-0.537940896847843","paper_counts_shrunk_log2fc":"-0.522620977996862","paper_counts_padj":"0.0033665751565914","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma08_g28260 | 1 | 1 | RNA and ribosome biogenesis | GO:0006353 | DNA-templated transcription termination | 0 | -- | SAP-like protein BP-73 | PREDICTED: SAP-like protein BP-73 [Musa acuminata subsp. malaccensis] | 0.478339761164731 | 0.339628872443094 | 0.603415395179115 | -0.32309389859166 | -0.296718604219112 | 0.387717102137916 | -0.467551326861477 | -0.429810102927426 | 0.261313623807845 | -0.513401393899625 | -0.49403990184119 | 0.0218964653983011 | -0.537940896847843 | -0.522620977996862 | 0.0033665751565914 | True | True


record_id: DS057_R00192
dataset_id: DS057
record_json:
{"gene_id":"Ma10_g01310","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006353 | DNA-templated transcription termination","all_three_pathway_count":"0","GO_annotation":"Molecular Function: double-stranded DNA binding (GO:0003690);; Cellular Component: mitochondrion (GO:0005739);; Biological Process: regulation of transcription, DNA-templated (GO:0006355);; ","Swiss_Prot_annotation":"Transcription termination factor MTEF1, chloroplastic","NR_annotation":"PREDICTED: uncharacterized protein LOC103974995 [Musa acuminata subsp. malaccensis]","recovery_log2fc":"0.392232230250872","recovery_shrunk_log2fc":"0.279854751313018","recovery_padj":"0.701741441232642","reciprocal_log2fc":"-0.328210417944574","reciprocal_shrunk_log2fc":"-0.31692224377853","reciprocal_padj":"0.122768671498926","exclude_pair_log2fc":"-0.388392152701004","exclude_pair_shrunk_log2fc":"-0.359481207896097","exclude_pair_padj":"0.353419426221159","five_traceable_log2fc":"-0.360659027676304","five_traceable_shrunk_log2fc":"-0.347904069063814","five_traceable_padj":"0.116241942082179","paper_counts_log2fc":"-0.562267172313806","paper_counts_shrunk_log2fc":"-0.547190855768641","paper_counts_padj":"0.0014152800027072","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma10_g01310 | 1 | 1 | RNA and ribosome biogenesis | GO:0006353 | DNA-templated transcription termination | 0 | Molecular Function: double-stranded DNA binding (GO:0003690);; Cellular Component: mitochondrion (GO:0005739);; Biological Process: regulation of transcription, DNA-templated (GO:0006355);;  | Transcription termination factor MTEF1, chloroplastic | PREDICTED: uncharacterized protein LOC103974995 [Musa acuminata subsp. malaccensis] | 0.392232230250872 | 0.279854751313018 | 0.701741441232642 | -0.328210417944574 | -0.31692224377853 | 0.122768671498926 | -0.388392152701004 | -0.359481207896097 | 0.353419426221159 | -0.360659027676304 | -0.347904069063814 | 0.116241942082179 | -0.562267172313806 | -0.547190855768641 | 0.0014152800027072 | True | True


record_id: DS057_R00193
dataset_id: DS057
record_json:
{"gene_id":"Ma10_g23890","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0043169 | cation binding","all_three_pathway_count":"0","GO_annotation":"Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);; ","Swiss_Prot_annotation":"Probable protein phosphatase 2C 60","NR_annotation":"PREDICTED: probable protein phosphatase 2C 60 [Musa acuminata subsp. malaccensis] ","recovery_log2fc":"-5.31762457994891","recovery_shrunk_log2fc":"-0.361361999736718","recovery_padj":"","reciprocal_log2fc":"0.475132526086482","reciprocal_shrunk_log2fc":"0.451070765750601","reciprocal_padj":"0.0573769089757881","exclude_pair_log2fc":"0.601131146972132","exclude_pair_shrunk_log2fc":"0.556938129887329","exclude_pair_padj":"0.0924882406806359","five_traceable_log2fc":"0.612257841673321","five_traceable_shrunk_log2fc":"0.592024099316941","five_traceable_padj":"0.0022533212776448","paper_counts_log2fc":"0.561045073961362","paper_counts_shrunk_log2fc":"0.555219949523013","paper_counts_padj":"6.46546939587343e-08","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma10_g23890 | 1 | 1 | RNA and ribosome biogenesis | GO:0043169 | cation binding | 0 | Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);;  | Probable protein phosphatase 2C 60 | PREDICTED: probable protein phosphatase 2C 60 [Musa acuminata subsp. malaccensis]  | -5.31762457994891 | -0.361361999736718 | 0.475132526086482 | 0.451070765750601 | 0.0573769089757881 | 0.601131146972132 | 0.556938129887329 | 0.0924882406806359 | 0.612257841673321 | 0.592024099316941 | 0.0022533212776448 | 0.561045073961362 | 0.555219949523013 | 6.46546939587343e-08 | True | True


record_id: DS057_R00194
dataset_id: DS057
record_json:
{"gene_id":"Ma10_g24090","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006353 | DNA-templated transcription termination","all_three_pathway_count":"0","GO_annotation":"--","Swiss_Prot_annotation":"Transcription termination factor MTERF15, mitochondrial","NR_annotation":"PREDICTED: transcription termination factor MTERF15, mitochondrial-like isoform X3 [Musa acuminata subsp. malaccensis]","recovery_log2fc":"0.653948154456563","recovery_shrunk_log2fc":"0.3075385664024","recovery_padj":"0.702373710382597","reciprocal_log2fc":"-0.555648895789016","reciprocal_shrunk_log2fc":"-0.508276346066083","reciprocal_padj":"0.102437768891112","exclude_pair_log2fc":"-0.717112535403984","exclude_pair_shrunk_log2fc":"-0.645669407813026","exclude_pair_padj":"0.0884402009797191","five_traceable_log2fc":"-0.733793010298884","five_traceable_shrunk_log2fc":"-0.699165685072871","five_traceable_padj":"0.0024246264903921","paper_counts_log2fc":"-0.947121973110942","paper_counts_shrunk_log2fc":"-0.670214656749268","paper_counts_padj":"0.215030746612352","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma10_g24090 | 1 | 1 | RNA and ribosome biogenesis | GO:0006353 | DNA-templated transcription termination | 0 | -- | Transcription termination factor MTERF15, mitochondrial | PREDICTED: transcription termination factor MTERF15, mitochondrial-like isoform X3 [Musa acuminata subsp. malaccensis] | 0.653948154456563 | 0.3075385664024 | 0.702373710382597 | -0.555648895789016 | -0.508276346066083 | 0.102437768891112 | -0.717112535403984 | -0.645669407813026 | 0.0884402009797191 | -0.733793010298884 | -0.699165685072871 | 0.0024246264903921 | -0.947121973110942 | -0.670214656749268 | 0.215030746612352 | True | True


record_id: DS057_R00195
dataset_id: DS057
record_json:
{"gene_id":"Ma10_g24170","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0006353 | DNA-templated transcription termination","all_three_pathway_count":"0","GO_annotation":"--","Swiss_Prot_annotation":"--","NR_annotation":"PREDICTED: uncharacterized protein LOC103969109 isoform X3 [Musa acuminata subsp. malaccensis] ","recovery_log2fc":"0.702388351952442","recovery_shrunk_log2fc":"0.496185523669475","recovery_padj":"0.357260287303601","reciprocal_log2fc":"-0.25843000769014","reciprocal_shrunk_log2fc":"-0.242300665446978","reciprocal_padj":"0.433382847467452","exclude_pair_log2fc":"-0.408668862577809","exclude_pair_shrunk_log2fc":"-0.370126082176206","exclude_pair_padj":"0.403011516755707","five_traceable_log2fc":"-0.331226821918495","five_traceable_shrunk_log2fc":"-0.311655854685271","five_traceable_padj":"0.302393569364923","paper_counts_log2fc":"0.0633097307476701","paper_counts_shrunk_log2fc":"0.0513123636765276","paper_counts_padj":"0.933445399140624","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma10_g24170 | 1 | 1 | RNA and ribosome biogenesis | GO:0006353 | DNA-templated transcription termination | 0 | -- | -- | PREDICTED: uncharacterized protein LOC103969109 isoform X3 [Musa acuminata subsp. malaccensis]  | 0.702388351952442 | 0.496185523669475 | 0.357260287303601 | -0.25843000769014 | -0.242300665446978 | 0.433382847467452 | -0.408668862577809 | -0.370126082176206 | 0.403011516755707 | -0.331226821918495 | -0.311655854685271 | 0.302393569364923 | 0.0633097307476701 | 0.0513123636765276 | 0.933445399140624 | True | True


record_id: DS057_R00196
dataset_id: DS057
record_json:
{"gene_id":"Ma11_g10690","robust_pathway_count":"1","robust_module_count":"1","modules":"RNA and ribosome biogenesis","pathways":"GO:0043169 | cation binding","all_three_pathway_count":"0","GO_annotation":"Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);; ","Swiss_Prot_annotation":"Probable protein phosphatase 2C 2","NR_annotation":"PREDICTED: probable protein phosphatase 2C 2 [Musa acuminata subsp. malaccensis]","recovery_log2fc":"-1.87519101911223","recovery_shrunk_log2fc":"-0.668583653952423","recovery_padj":"0.159863189463603","reciprocal_log2fc":"1.48884379215084","reciprocal_shrunk_log2fc":"1.40781222678708","reciprocal_padj":"3.65580008967027e-12","exclude_pair_log2fc":"1.49414076350764","exclude_pair_shrunk_log2fc":"1.33691222710347","exclude_pair_padj":"3.8124409534697e-05","five_traceable_log2fc":"1.48396976696975","five_traceable_shrunk_log2fc":"1.39992715704918","five_traceable_padj":"1.4426245127627201e-09","paper_counts_log2fc":"1.55114587885162","paper_counts_shrunk_log2fc":"1.50279322478571","paper_counts_padj":"1.3448583139687e-18","corrected_effect_direction_stable":"True","opposite_recovery_vs_corrected":"True"}

search_text:
Ma11_g10690 | 1 | 1 | RNA and ribosome biogenesis | GO:0043169 | cation binding | 0 | Molecular Function: protein serine/threonine phosphatase activity (GO:0004722);; Biological Process: protein dephosphorylation (GO:0006470);; Molecular Function: metal ion binding (GO:0046872);;  | Probable protein phosphatase 2C 2 | PREDICTED: probable protein phosphatase 2C 2 [Musa acuminata subsp. malaccensis] | -1.87519101911223 | -0.668583653952423 | 0.159863189463603 | 1.48884379215084 | 1.40781222678708 | 3.65580008967027e-12 | 1.49414076350764 | 1.33691222710347 | 3.8124409534697e-05 | 1.48396976696975 | 1.39992715704918 | 1.4426245127627201e-09 | 1.55114587885162 | 1.50279322478571 | 1.3448583139687e-18 | True | True


record_id: DS058_R00001
dataset_id: DS058
record_json:
{"pathway":"GO:0005730 | nucleolus","term":"nucleolus","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"2.1206831080103","padj_temperature_recovery":"6.24273736282246e-08","NES_reciprocal_swap":"-1.9107371877008","padj_reciprocal_swap":"1.21840096208526e-06","NES_exclude_pair":"-1.88301092574268","padj_exclude_pair":"1.4719824371887e-06","NES_five_traceable":"-1.76172649540172","padj_five_traceable":"1.79918844751054e-05","NES_paper_count_matrix":"-2.02682618160193","padj_paper_count_matrix":"6.87828479073893e-08","recovery_plus_corrected_intersection_n":"40"}

search_text:
GO:0005730 | nucleolus | nucleolus | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 2.1206831080103 | 6.24273736282246e-08 | -1.9107371877008 | 1.21840096208526e-06 | -1.88301092574268 | 1.4719824371887e-06 | -1.76172649540172 | 1.79918844751054e-05 | -2.02682618160193 | 6.87828479073893e-08 | 40


record_id: DS058_R00002
dataset_id: DS058
record_json:
{"pathway":"GO:0005874 | microtubule","term":"microtubule","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.9409710266405","padj_temperature_recovery":"0.0001255503233988","NES_reciprocal_swap":"-2.8167621294575","padj_reciprocal_swap":"4.0812561075970005e-21","NES_exclude_pair":"-2.29777671662301","padj_exclude_pair":"3.3033503975783e-11","NES_five_traceable":"-2.33125871116978","padj_five_traceable":"1.1442242396949298e-11","NES_paper_count_matrix":"-2.26541400020697","padj_paper_count_matrix":"9.959658254139809e-11","recovery_plus_corrected_intersection_n":"37"}

search_text:
GO:0005874 | microtubule | microtubule | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.9409710266405 | 0.0001255503233988 | -2.8167621294575 | 4.0812561075970005e-21 | -2.29777671662301 | 3.3033503975783e-11 | -2.33125871116978 | 1.1442242396949298e-11 | -2.26541400020697 | 9.959658254139809e-11 | 37


record_id: DS058_R00003
dataset_id: DS058
record_json:
{"pathway":"GO:0000278 | mitotic cell cycle","term":"mitotic cell cycle","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"2.13716616365524","padj_temperature_recovery":"0.0004661958861068","NES_reciprocal_swap":"-2.60189392196261","padj_reciprocal_swap":"3.62136683635587e-09","NES_exclude_pair":"-2.28161847039042","padj_exclude_pair":"3.48116121807976e-06","NES_five_traceable":"-2.29665073115728","padj_five_traceable":"1.47362977781521e-06","NES_paper_count_matrix":"-2.30801348028803","padj_paper_count_matrix":"1.10516190151569e-06","recovery_plus_corrected_intersection_n":"12"}

search_text:
GO:0000278 | mitotic cell cycle | mitotic cell cycle | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 2.13716616365524 | 0.0004661958861068 | -2.60189392196261 | 3.62136683635587e-09 | -2.28161847039042 | 3.48116121807976e-06 | -2.29665073115728 | 1.47362977781521e-06 | -2.30801348028803 | 1.10516190151569e-06 | 12


record_id: DS058_R00004
dataset_id: DS058
record_json:
{"pathway":"GO:0001522 | pseudouridine synthesis","term":"pseudouridine synthesis","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"2.13102229642782","padj_temperature_recovery":"0.0020409284856812","NES_reciprocal_swap":"-1.76879419523492","padj_reciprocal_swap":"0.0178209955260757","NES_exclude_pair":"-1.81814940285251","padj_exclude_pair":"0.039890466903552","NES_five_traceable":"-1.78620433763653","padj_five_traceable":"0.0157957366419706","NES_paper_count_matrix":"-1.81892842572409","padj_paper_count_matrix":"0.0283261992441942","recovery_plus_corrected_intersection_n":"10"}

search_text:
GO:0001522 | pseudouridine synthesis | pseudouridine synthesis | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 2.13102229642782 | 0.0020409284856812 | -1.76879419523492 | 0.0178209955260757 | -1.81814940285251 | 0.039890466903552 | -1.78620433763653 | 0.0157957366419706 | -1.81892842572409 | 0.0283261992441942 | 10


record_id: DS058_R00005
dataset_id: DS058
record_json:
{"pathway":"GO:0007017 | microtubule-based process","term":"microtubule-based process","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.99809792166502","padj_temperature_recovery":"0.0030792256855029","NES_reciprocal_swap":"-2.01863224674914","padj_reciprocal_swap":"0.0006282268059185","NES_exclude_pair":"-1.64737550922211","padj_exclude_pair":"0.0305579364005138","NES_five_traceable":"-1.73747958438122","padj_five_traceable":"0.0115167289327478","NES_paper_count_matrix":"-1.69537339112081","padj_paper_count_matrix":"0.0201975831574895","recovery_plus_corrected_intersection_n":"11"}

search_text:
GO:0007017 | microtubule-based process | microtubule-based process | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.99809792166502 | 0.0030792256855029 | -2.01863224674914 | 0.0006282268059185 | -1.64737550922211 | 0.0305579364005138 | -1.73747958438122 | 0.0115167289327478 | -1.69537339112081 | 0.0201975831574895 | 11


record_id: DS058_R00006
dataset_id: DS058
record_json:
{"pathway":"GO:0008033 | tRNA processing","term":"tRNA processing","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.96361327778007","padj_temperature_recovery":"0.003389222204759","NES_reciprocal_swap":"-1.80099479717451","padj_reciprocal_swap":"0.003212656315103","NES_exclude_pair":"-1.60081003436903","padj_exclude_pair":"0.0203834519613347","NES_five_traceable":"-1.50502723765044","padj_five_traceable":"0.0342765524977344","NES_paper_count_matrix":"-1.45248053283375","padj_paper_count_matrix":"0.10262833621976","recovery_plus_corrected_intersection_n":"14"}

search_text:
GO:0008033 | tRNA processing | tRNA processing | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 1.96361327778007 | 0.003389222204759 | -1.80099479717451 | 0.003212656315103 | -1.60081003436903 | 0.0203834519613347 | -1.50502723765044 | 0.0342765524977344 | -1.45248053283375 | 0.10262833621976 | 14


record_id: DS058_R00007
dataset_id: DS058
record_json:
{"pathway":"GO:0006364 | rRNA processing","term":"rRNA processing","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.76086223590816","padj_temperature_recovery":"0.0039508164079357","NES_reciprocal_swap":"-1.93312205997732","padj_reciprocal_swap":"7.95680312505607e-05","NES_exclude_pair":"-1.68143559694147","padj_exclude_pair":"0.0027724195448119","NES_five_traceable":"-1.67559813790884","padj_five_traceable":"0.003391199659785","NES_paper_count_matrix":"-1.6860569209096","padj_paper_count_matrix":"0.0069868553171655","recovery_plus_corrected_intersection_n":"27"}

search_text:
GO:0006364 | rRNA processing | rRNA processing | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 1.76086223590816 | 0.0039508164079357 | -1.93312205997732 | 7.95680312505607e-05 | -1.68143559694147 | 0.0027724195448119 | -1.67559813790884 | 0.003391199659785 | -1.6860569209096 | 0.0069868553171655 | 27


record_id: DS058_R00008
dataset_id: DS058
record_json:
{"pathway":"GO:0032040 | small-subunit processome","term":"small-subunit processome","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.91302594219346","padj_temperature_recovery":"0.0108289262412544","NES_reciprocal_swap":"-2.03063559857253","padj_reciprocal_swap":"0.0004744444280208","NES_exclude_pair":"-1.97538267412819","padj_exclude_pair":"0.0026494299156851","NES_five_traceable":"-1.90379057833319","padj_five_traceable":"0.0041044274799144","NES_paper_count_matrix":"-2.172408031103","padj_paper_count_matrix":"0.0001012316304667","recovery_plus_corrected_intersection_n":"13"}

search_text:
GO:0032040 | small-subunit processome | small-subunit processome | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 1.91302594219346 | 0.0108289262412544 | -2.03063559857253 | 0.0004744444280208 | -1.97538267412819 | 0.0026494299156851 | -1.90379057833319 | 0.0041044274799144 | -2.172408031103 | 0.0001012316304667 | 13


record_id: DS058_R00009
dataset_id: DS058
record_json:
{"pathway":"GO:0042254 | ribosome biogenesis","term":"ribosome biogenesis","module":"RNA and ribosome biogenesis","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.71400876302673","padj_temperature_recovery":"0.013768132936072","NES_reciprocal_swap":"-1.74156104026717","padj_reciprocal_swap":"0.0043844769296526","NES_exclude_pair":"-1.75129267789159","padj_exclude_pair":"0.0034304108311275","NES_five_traceable":"-1.6294709642687","padj_five_traceable":"0.0058091559034001","NES_paper_count_matrix":"-1.78504279489921","padj_paper_count_matrix":"0.0031895460923032","recovery_plus_corrected_intersection_n":"17"}

search_text:
GO:0042254 | ribosome biogenesis | ribosome biogenesis | RNA and ribosome biogenesis | all_three_corrected_plus_recovery | 3 | opposite | 1.71400876302673 | 0.013768132936072 | -1.74156104026717 | 0.0043844769296526 | -1.75129267789159 | 0.0034304108311275 | -1.6294709642687 | 0.0058091559034001 | -1.78504279489921 | 0.0031895460923032 | 17


record_id: DS058_R00010
dataset_id: DS058
record_json:
{"pathway":"GO:0006633 | fatty acid biosynthetic process","term":"fatty acid biosynthetic process","module":"Lipid-ethylene metabolism","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"-1.76655644442737","padj_temperature_recovery":"0.0145179957210494","NES_reciprocal_swap":"2.14274008024506","padj_reciprocal_swap":"1.49878719801469e-06","NES_exclude_pair":"1.94828823180111","padj_exclude_pair":"0.0001605737057503","NES_five_traceable":"1.92653430766235","padj_five_traceable":"0.0001422074633696","NES_paper_count_matrix":"2.09350813157457","padj_paper_count_matrix":"7.09963072052372e-06","recovery_plus_corrected_intersection_n":"14"}

search_text:
GO:0006633 | fatty acid biosynthetic process | fatty acid biosynthetic process | Lipid-ethylene metabolism | all_three_corrected_plus_recovery | 3 | opposite | -1.76655644442737 | 0.0145179957210494 | 2.14274008024506 | 1.49878719801469e-06 | 1.94828823180111 | 0.0001605737057503 | 1.92653430766235 | 0.0001422074633696 | 2.09350813157457 | 7.09963072052372e-06 | 14


record_id: DS058_R00011
dataset_id: DS058
record_json:
{"pathway":"GO:0003777 | microtubule motor activity","term":"microtubule motor activity","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.8204153845088","padj_temperature_recovery":"0.0168742467432214","NES_reciprocal_swap":"-2.73544740880734","padj_reciprocal_swap":"1.14461598899202e-11","NES_exclude_pair":"-2.42280815684113","padj_exclude_pair":"6.92455648618915e-08","NES_five_traceable":"-2.32151076215784","padj_five_traceable":"2.07273078592305e-06","NES_paper_count_matrix":"-2.30706701764527","padj_paper_count_matrix":"1.01226461231368e-06","recovery_plus_corrected_intersection_n":"17"}

search_text:
GO:0003777 | microtubule motor activity | microtubule motor activity | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.8204153845088 | 0.0168742467432214 | -2.73544740880734 | 1.14461598899202e-11 | -2.42280815684113 | 6.92455648618915e-08 | -2.32151076215784 | 2.07273078592305e-06 | -2.30706701764527 | 1.01226461231368e-06 | 17


record_id: DS058_R00012
dataset_id: DS058
record_json:
{"pathway":"GO:0007018 | microtubule-based movement","term":"microtubule-based movement","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.8204153845088","padj_temperature_recovery":"0.0168742467432214","NES_reciprocal_swap":"-2.73544740880734","padj_reciprocal_swap":"1.14461598899202e-11","NES_exclude_pair":"-2.42280815684113","padj_exclude_pair":"6.92455648618915e-08","NES_five_traceable":"-2.32151076215784","padj_five_traceable":"2.07273078592305e-06","NES_paper_count_matrix":"-2.30706701764527","padj_paper_count_matrix":"1.01226461231368e-06","recovery_plus_corrected_intersection_n":"17"}

search_text:
GO:0007018 | microtubule-based movement | microtubule-based movement | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.8204153845088 | 0.0168742467432214 | -2.73544740880734 | 1.14461598899202e-11 | -2.42280815684113 | 6.92455648618915e-08 | -2.32151076215784 | 2.07273078592305e-06 | -2.30706701764527 | 1.01226461231368e-06 | 17


record_id: DS058_R00013
dataset_id: DS058
record_json:
{"pathway":"GO:0009873 | ethylene-activated signaling pathway","term":"ethylene-activated signaling pathway","module":"Lipid-ethylene metabolism","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"-1.76241278963841","padj_temperature_recovery":"0.0204101197179376","NES_reciprocal_swap":"2.63735221271295","padj_reciprocal_swap":"1.71940630773866e-14","NES_exclude_pair":"2.51489995047432","padj_exclude_pair":"1.56844157901933e-11","NES_five_traceable":"2.49652740865724","padj_five_traceable":"1.8058634854877298e-11","NES_paper_count_matrix":"2.522278855344","padj_paper_count_matrix":"1.13598308675035e-11","recovery_plus_corrected_intersection_n":"13"}

search_text:
GO:0009873 | ethylene-activated signaling pathway | ethylene-activated signaling pathway | Lipid-ethylene metabolism | all_three_corrected_plus_recovery | 3 | opposite | -1.76241278963841 | 0.0204101197179376 | 2.63735221271295 | 1.71940630773866e-14 | 2.51489995047432 | 1.56844157901933e-11 | 2.49652740865724 | 1.8058634854877298e-11 | 2.522278855344 | 1.13598308675035e-11 | 13


record_id: DS058_R00014
dataset_id: DS058
record_json:
{"pathway":"GO:0000082 | G1/S transition of mitotic cell cycle","term":"G1/S transition of mitotic cell cycle","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.78324638489421","padj_temperature_recovery":"0.0293041994829991","NES_reciprocal_swap":"-2.71431795609306","padj_reciprocal_swap":"4.90787121787048e-10","NES_exclude_pair":"-2.63176933007605","padj_exclude_pair":"7.522938135456811e-10","NES_five_traceable":"-2.6325270838418","padj_five_traceable":"1.14569693734384e-09","NES_paper_count_matrix":"-2.58478041585223","padj_paper_count_matrix":"1.08505046776428e-09","recovery_plus_corrected_intersection_n":"7"}

search_text:
GO:0000082 | G1/S transition of mitotic cell cycle | G1/S transition of mitotic cell cycle | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.78324638489421 | 0.0293041994829991 | -2.71431795609306 | 4.90787121787048e-10 | -2.63176933007605 | 7.522938135456811e-10 | -2.6325270838418 | 1.14569693734384e-09 | -2.58478041585223 | 1.08505046776428e-09 | 7


record_id: DS058_R00015
dataset_id: DS058
record_json:
{"pathway":"GO:0006631 | fatty acid metabolic process","term":"fatty acid metabolic process","module":"Lipid-ethylene metabolism","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"-1.60021851790697","padj_temperature_recovery":"0.0328006482022303","NES_reciprocal_swap":"2.06567249309023","padj_reciprocal_swap":"4.06956749411358e-06","NES_exclude_pair":"1.85121394778142","padj_exclude_pair":"0.0006870392746355","NES_five_traceable":"1.87280040608725","padj_five_traceable":"0.0004544029135276","NES_paper_count_matrix":"2.15326929328676","padj_paper_count_matrix":"1.10516190151569e-06","recovery_plus_corrected_intersection_n":"10"}

search_text:
GO:0006631 | fatty acid metabolic process | fatty acid metabolic process | Lipid-ethylene metabolism | all_three_corrected_plus_recovery | 3 | opposite | -1.60021851790697 | 0.0328006482022303 | 2.06567249309023 | 4.06956749411358e-06 | 1.85121394778142 | 0.0006870392746355 | 1.87280040608725 | 0.0004544029135276 | 2.15326929328676 | 1.10516190151569e-06 | 10


record_id: DS058_R00016
dataset_id: DS058
record_json:
{"pathway":"GO:0008017 | microtubule binding","term":"microtubule binding","module":"Cell cycle and microtubules","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"1.51223794819398","padj_temperature_recovery":"0.0352653652123321","NES_reciprocal_swap":"-2.78691883318048","padj_reciprocal_swap":"4.61610459597276e-18","NES_exclude_pair":"-2.32777230775312","padj_exclude_pair":"4.8396669000769496e-11","NES_five_traceable":"-2.31796622207588","padj_five_traceable":"1.55515618337479e-10","NES_paper_count_matrix":"-2.3181357885177","padj_paper_count_matrix":"2.35628808121967e-10","recovery_plus_corrected_intersection_n":"20"}

search_text:
GO:0008017 | microtubule binding | microtubule binding | Cell cycle and microtubules | all_three_corrected_plus_recovery | 3 | opposite | 1.51223794819398 | 0.0352653652123321 | -2.78691883318048 | 4.61610459597276e-18 | -2.32777230775312 | 4.8396669000769496e-11 | -2.31796622207588 | 1.55515618337479e-10 | -2.3181357885177 | 2.35628808121967e-10 | 20


record_id: DS058_R00017
dataset_id: DS058
record_json:
{"pathway":"GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor","term":"oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor","module":"Lipid-ethylene metabolism","evidence_tier":"all_three_corrected_plus_recovery","corrected_fdr_count":"3","recovery_relation":"opposite","NES_temperature_recovery":"-1.62142342962881","padj_temperature_recovery":"0.0408102118260047","NES_reciprocal_swap":"1.75208498294435","padj_reciprocal_swap":"0.0023225247293346","NES_exclude_pair":"1.58304278491156","padj_exclude_pair":"0.0240544006538693","NES_five_traceable":"1.65803400673096","padj_five_traceable":"0.0125172273372487","NES_paper_count_matrix":"1.74741837995653","padj_paper_count_matrix":"0.0046259172034942","recovery_plus_corrected_intersection_n":"10"}

search_text:
GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | Lipid-ethylene metabolism | all_three_corrected_plus_recovery | 3 | opposite | -1.62142342962881 | 0.0408102118260047 | 1.75208498294435 | 0.0023225247293346 | 1.58304278491156 | 0.0240544006538693 | 1.65803400673096 | 0.0125172273372487 | 1.74741837995653 | 0.0046259172034942 | 10


record_id: DS058_R00018
dataset_id: DS058
record_json:
{"pathway":"GO:0006353 | DNA-templated transcription termination","term":"DNA-templated transcription termination","module":"RNA and ribosome biogenesis","evidence_tier":"two_of_three_corrected_plus_recovery","corrected_fdr_count":"2","recovery_relation":"opposite","NES_temperature_recovery":"2.04639843583374","padj_temperature_recovery":"0.0004661958861068","NES_reciprocal_swap":"-1.87784966362148","padj_reciprocal_swap":"0.0017872854913068","NES_exclude_pair":"-1.46396535229458","padj_exclude_pair":"0.070509168976831","NES_five_traceable":"-1.46807851986047","padj_five_traceable":"0.0495862417939395","NES_paper_count_matrix":"-1.15445115555461","padj_paper_count_matrix":"0.393655828707375","recovery_plus_corrected_intersection_n":"12"}

search_text:
GO:0006353 | DNA-templated transcription termination | DNA-templated transcription termination | RNA and ribosome biogenesis | two_of_three_corrected_plus_recovery | 2 | opposite | 2.04639843583374 | 0.0004661958861068 | -1.87784966362148 | 0.0017872854913068 | -1.46396535229458 | 0.070509168976831 | -1.46807851986047 | 0.0495862417939395 | -1.15445115555461 | 0.393655828707375 | 12


record_id: DS058_R00019
dataset_id: DS058
record_json:
{"pathway":"GO:0006950 | response to stress","term":"response to stress","module":"RNA and ribosome biogenesis","evidence_tier":"two_of_three_corrected_plus_recovery","corrected_fdr_count":"2","recovery_relation":"opposite","NES_temperature_recovery":"-1.58000939184623","padj_temperature_recovery":"0.042493319612567","NES_reciprocal_swap":"1.53262633053159","padj_reciprocal_swap":"0.0170682021765589","NES_exclude_pair":"1.52113376017176","padj_exclude_pair":"0.0329251261823051","NES_five_traceable":"1.40689964896814","padj_five_traceable":"0.0875401580228665","NES_paper_count_matrix":"1.48969240688639","padj_paper_count_matrix":"0.0447357377738985","recovery_plus_corrected_intersection_n":"10"}

search_text:
GO:0006950 | response to stress | response to stress | RNA and ribosome biogenesis | two_of_three_corrected_plus_recovery | 2 | opposite | -1.58000939184623 | 0.042493319612567 | 1.53262633053159 | 0.0170682021765589 | 1.52113376017176 | 0.0329251261823051 | 1.40689964896814 | 0.0875401580228665 | 1.48969240688639 | 0.0447357377738985 | 10


record_id: DS058_R00020
dataset_id: DS058
record_json:
{"pathway":"GO:0009086 | methionine biosynthetic process","term":"methionine biosynthetic process","module":"RNA and ribosome biogenesis","evidence_tier":"two_of_three_corrected_plus_recovery","corrected_fdr_count":"2","recovery_relation":"opposite","NES_temperature_recovery":"-1.82337178485022","padj_temperature_recovery":"0.0438501643129307","NES_reciprocal_swap":"1.56741469788622","padj_reciprocal_swap":"0.0946941454598933","NES_exclude_pair":"1.79808634510616","padj_exclude_pair":"0.0323454051967725","NES_five_traceable":"1.73697418856028","padj_five_traceable":"0.0439179995313445","NES_paper_count_matrix":"","padj_paper_count_matrix":"","recovery_plus_corrected_intersection_n":"1"}

search_text:
GO:0009086 | methionine biosynthetic process | methionine biosynthetic process | RNA and ribosome biogenesis | two_of_three_corrected_plus_recovery | 2 | opposite | -1.82337178485022 | 0.0438501643129307 | 1.56741469788622 | 0.0946941454598933 | 1.79808634510616 | 0.0323454051967725 | 1.73697418856028 | 0.0439179995313445 | 1


record_id: DS058_R00021
dataset_id: DS058
record_json:
{"pathway":"GO:0043169 | cation binding","term":"cation binding","module":"RNA and ribosome biogenesis","evidence_tier":"two_of_three_corrected_plus_recovery","corrected_fdr_count":"2","recovery_relation":"opposite","NES_temperature_recovery":"-1.57079251886625","padj_temperature_recovery":"0.0458755013755481","NES_reciprocal_swap":"1.65062980201477","padj_reciprocal_swap":"0.0185589417868649","NES_exclude_pair":"1.60955159506706","padj_exclude_pair":"0.056423639749051","NES_five_traceable":"1.69271401732756","padj_five_traceable":"0.0105978735551023","NES_paper_count_matrix":"1.67445445296922","padj_paper_count_matrix":"0.022919810187143","recovery_plus_corrected_intersection_n":"9"}

search_text:
GO:0043169 | cation binding | cation binding | RNA and ribosome biogenesis | two_of_three_corrected_plus_recovery | 2 | opposite | -1.57079251886625 | 0.0458755013755481 | 1.65062980201477 | 0.0185589417868649 | 1.60955159506706 | 0.056423639749051 | 1.69271401732756 | 0.0105978735551023 | 1.67445445296922 | 0.022919810187143 | 9


# stage_gates

gate_id: G1
gate_name: Pollen formation and collection
input_signal: Pollen quantity, staining viability, size state and developmental weather window
functional_endpoint: Pollen available for functional testing
failure_mode: Low supply, stain-positive but functionally weak pollen, or an unstable collection window
evidence_grade: B
dataset_ids: DS043;DS044;DS045
decision_action: Retain calibration sets by genotype and month, then prioritize transferable models.
claim_boundary: Do not treat a weather association in one cohort as a universal optimum.
key_result:
Climate association does not replace transfer to withheld months; genome group helps prediction for unseen genotypes.


gate_id: G3
gate_name: Pistil traversal and fertilization arrival
input_signal: Stigma receptivity, pollination timing, tube length and ovary arrival
functional_endpoint: Pollen tubes reach the ovary or ovule
failure_mode: Post-germination arrest, tissue-length differences or cross incompatibility
evidence_grade: B
dataset_ids: DS049;DS050
decision_action: Evaluate stigma-to-ovary progression by cross and time series, not endpoint length alone.
claim_boundary: Do not split aggregated worksheets into independent biological replicates.
key_result:
In vitro germination does not guarantee rapid pistil traversal; genotype class, timing and cross context alter progression.


gate_id: G4
gate_name: Seed and embryo recovery
input_signal: Any-seed probability, seed intensity after success, embryo extraction and germination
functional_endpoint: Recoverable embryos or seedlings
failure_mode: Zero seed, embryo abortion or low conditional output after a successful cross
evidence_grade: B
dataset_ids: DS052;DS053;DS017
claim_boundary: An intervention that raises conditional seed count does not necessarily reduce zero-seed failure.
key_result:
Seed initiation and seed intensity after success represent different constraints and must be reported separately.

decision_action:
Select a probability or conditional-intensity model for the decision endpoint and preserve its denominator.


gate_id: G5
gate_name: Elite triploid recovery
input_signal: Parental ploidy roles, structural heterogeneity, yield, maturity, plant architecture and QTL
functional_endpoint: Superior progeny meeting multi-trait targets in later cycles
failure_mode: No mean gain, a small elite tail, structural linkage or failure of cross-programme model transfer
evidence_grade: B
dataset_ids: DS011;DS012;DS013;DS014;DS031;DS037;DS038;DS041
key_result:
Structural heterogeneity increases family dispersion but not means; frozen model benefit varies by cohort; long-term records identify 27 advanced hybrids and one release.

decision_action:
Secure the first four gates, audit auxiliary-trait repeatability and validate in the target programme.

claim_boundary:
Parent-level advancement association is not individual prediction, and the four-cohort relation is not a universal threshold.


# scientific_claims

claim_id: C05
domain: duplicate_architecture
claim_status: reproduced
evidence_grade: B
supporting_dataset_ids: DS001;DS003
observed_scope: Matched null models across multiple thresholds
allowed_interpretation: Supports structural differences between capacity and deployment branches.
prohibited_interpretation: Do not attribute the pattern directly to a named WGD event.
claim_text:
The rRNA-biogenesis branch is depleted for proximal and syntenic duplicates relative to matched backgrounds.


claim_id: C09
domain: structural_dispersion
claim_status: reproduced
evidence_grade: B
supporting_dataset_ids: DS011;DS010
observed_scope: Thirty-two families plus threshold and leave-one-family sensitivity tests
allowed_interpretation: Use dispersion to plan family size for selection capacity.
prohibited_interpretation: Do not describe wider dispersion as higher breeding value.
claim_text:
Parental structural heterogeneity is associated with family multi-trait dispersion but not family means.


claim_id: C13
domain: breeding_validation
claim_status: sensitivity_supported
evidence_grade: B
supporting_dataset_ids: DS023;DS024;DS019
observed_scope: 486 progeny, 66 unseen families and two later-cycle outcomes
allowed_interpretation: Supports prospective evaluation within the same breeding programme.
prohibited_interpretation: Do not replace family-bootstrap intervals with point estimates or claim universal superiority.
claim_text:
The locked stage-aware model improves later-cycle elite ranking in completely unseen CIRAD families.


claim_id: C14
domain: transportability
claim_text: Benefit from the frozen multi-trait index varies with cohort and auxiliary-trait repeatability.
claim_status: sensitivity_supported
evidence_grade: B
supporting_dataset_ids: DS031;DS036;DS037;DS035
observed_scope: Complete units from CIRAD, Sendusu, Arusha and NM cohorts
prohibited_interpretation: Do not present the four-cohort rank relation as a confirmed transfer law.
allowed_interpretation:
Audit maturity repeatability, protocol compatibility and target-cohort performance before deployment.


claim_id: C15
domain: resource_allocation
claim_status: reproduced
evidence_grade: B
supporting_dataset_ids: DS022
observed_scope: Families with at least five complete progeny under a fixed offspring budget
allowed_interpretation: Report capture, elite yield per 100 progeny and parental diversity together.
prohibited_interpretation: Do not use unequal evaluation totals to claim superior allocation.
claim_text:
Family-size correction increases absolute elite capture mainly by evaluating more offspring, not by improving resource efficiency.


claim_id: C16
domain: historical_advancement
claim_text: Historical maternal seed initiation is associated with named NARITA advancement output.
claim_status: sensitivity_supported
evidence_grade: B
supporting_dataset_ids: DS038;DS041;DS039
observed_scope: Ten tetraploid mothers; 24 of 27 advanced hybrids linked to 17 crosses; one release
allowed_interpretation:
Provides a parent-level bridge from reproductive output to formal advancement and guides prospective label collection.

prohibited_interpretation:
Do not claim individual advancement prediction, causal gain or complete linkage for all 12,000 entries.


# validation_cohorts

cohort_id: VC01
cohort_name: CIRAD development
programme: CIRAD
validation_role: development
outcome: future_top20
outcome_definition: Top 20% of the geometric mean of cycle-two yield and earliness favorable ranks
unseen_family_rule: Families represented in the genotyped development cohort
source_dataset_id: DS018
limitation: Used only to lock weights and probability calibration; it is not an external test set.
trait_scaling:
Within-candidate-cohort favorable percentile ranks; training-reference scaling retained as sensitivity analysis


cohort_id: VC04
cohort_name: IITA Sendusu external
programme: IITA
validation_role: external_programme_validation
outcome: future_top20
outcome_definition: Top 20% of the geometric mean of cycle-two yield and earliness favorable ranks
unseen_family_rule: Independent programme, trial and family keys; no model refitting
source_dataset_id: DS021
limitation:
Only anonymous outcomes and locked probabilities are redistributed; raw identifiers and traits remain at MusaBase.


# prediction_models

model_id: M3
model_name: Training-derived stage-aware
application_level: individual
input_traits: yield; earliness; robustness; harvest leaves
locked_cohort_id: VC01
limitation: Benefit varied across unseen CIRAD, Sendusu, Arusha and NM validation cohorts.
deployment_rule:
Non-negative geometric index; weights and probability calibration locked in family-grouped development analysis


