input/1_PIS_dinar_comparison_l1-wt.txt Version 1
_p_SUSPHIRE/_I_T21_SXPsysbio/_S_P4_DiNAR/_A_PIS-DiNAR/
SEEK ID: https://fairdomhub.org/data_files/5112?version=1
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input/1_PIS_dinar_comparison_l1-wt.txt
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probeID clade LogFC_l1.wt pAdj_l1.wt g15680 4CLL -0.22 0.896 g7226 ACH -0.15 0.8874 g94763 ACO -1.02 0.9298 g110 ACS1,2,6 -0.35 0.9193 g98107 ACX1,5 -0.3 0.8268 g74214 ADT 0.34 0.831 g48179 AGO1,5,7,10 0.62 0.8788 g24790 AOC -0.38 0.8461 g68176 AOS -0.18 0.9325 g74581 APX1,2 -0.5 0.8268 g58109 APX3 -0.67 0.8268 g41270 APX4 -0.34 0.9329 g58903 ASK 0.02 0.9939 g46963 ATPB 0.19 0.929 g73355 bHLH -0.11 0.9142 g48033 CAMTA 0.1 0.925 g81197 CAT1,2,3 -0.05 0.9916 g47201 CLH 0.16 0.9463 g22769 CM -0.17 0.9414 g2366 CML42 -0.38 0.9034 g33598 COI1 0.28 0.832 g115444 CPK4,5,6,11 0.14 0.8798 g60724 CRT1,2 0.53 0.8268 g96456 CRT3 0.04 0.9826 g103432 CTR 0.19 0.8777 g29012 CTS 0.23 0.8268 g90041 CUL 0.02 0.9887 g8133 CYP94 0.19 0.9138 g86929 DXPS 0.38 0.9595 g14686 EBF 0.12 0.9431 g12642 EDF 0.07 0.9838 g29542 EIN2 0.12 0.9491 g90995 EIN3(EIL1) 0.52 0.832 g1650 ERF1,2 0.18 0.9285 g97252 ERF104 -0.44 0.832 g37276 ERF105 0.22 0.936 g64272 ETR 0.02 0.9892 g33365 GRAS2 -0.03 0.9926 g119629 GST -0.14 0.9413 g67142 HMA 0.57 0.8932 g92328 ICS 0.55 0.8268 g99312 JAR -0.1 0.9573 g94936 JAZ1,2,5,6 -0.52 0.885 g33245 JMT -0.54 0.8268 g21233 LOX -1.24 0.8268 g47512 MES -0.07 0.9643 g70445 MFP -0.2 0.8913 g110094 MIND1 0.32 0.8268 g9063 MOS 0.95 0.0179 g97771 MPK4 0.05 0.9782 g8740 MPK6 -0.02 0.9825 g2832 MYB113 0.89 0.9389 g34850 MYB44,70,73 -0.51 0.9079 g99248 MYC -1.53 0.8268 g73486 NADPH-oxidase -0.13 0.9389 g119355 NDA -0.06 0.9907 g23352 NDB -0.08 0.9888 g97425 NDC -0.11 0.8945 g120824 OMR1 -0.26 0.8842 g65921 OPR -0.33 0.9162 g114938 PA -0.25 0.832 g120999 PAL 0.34 0.8384 g87733 PR1 -0.45 0.992 g24398 PR3 0.24 0.9389 g60136 PR4 0.05 0.9974 g8456 PSAK -0.48 0.9371 g119538 RBCL 0.22 0.8719 g24746 RBCS -0.4 0.9574 g125569 RGA1,2 -0.04 0.9686 g99438 RH 0.33 0.8268 g98443 RTE1 0.07 0.9793 g64887 SAHH 0.08 0.9702 g60842 SAMS 0.14 0.9062 g61550 SERK 0.39 0.8268 g95192 SOD -0.45 0.8315 g88154 TGA2,5,6 -0.09 0.9469 g132812 TRX-H -0.39 0.854 g128834 WAK 0.76 0.8268 g110530 WD40 -0.34 0.8351 g18994 WRKY11,17 -0.16 0.9384
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Created: 9th Apr 2022 at 20:16
Last updated: 21st Sep 2022 at 10:45
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Version 1 (earliest) Created 9th Apr 2022 at 20:16 by Marko Petek
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https://orcid.org/0000-0003-3644-7827PhD in Biotechnology, Research Associate at Department of Biotechnology and Systems Biology, National Institute of Biology
National Institute of Biology, Department of Biotechnology and Systems Biology projects
Projects: HYp - Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato, pISA-tree, MOA - Multiomics analysis of potato response to Potato virus Y (PVY) infection, SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, INDIE - Biotechnological production of sustainable indole, _p_stRT, ADAPT - Accelerated Development of multiple-stress tolerAnt PoTato, _p_RNAinVAL, tst, tst2, Playground
Web page: http://www.nib.si/eng/index.php/departments/department-of-biotechnology-and-systems-biology
SUSPHIRE aims to provide a sustainable, low-cost biomanufacturing platform for the commercial production of insect pheromones.
Synthetic biology data management spreadsheet: https://fairdomhub.org/data_files/6036
Programme: NIBSys
Public web page: http://susphire.info/susphireproject/
Start date: 1st Apr 2018
End date: 30th Sep 2021
Short Name: T21_SXPsysbio Title: Use a systems biology approach to identify regulatory bottlenecks in SxPv1 Description: Samples from SXPv1.0 plants as well as sister nulls (progeny from the original transgenic event in which the transgene has segregated) and wild type will be grown and leaf samples taken for RNA extraction and profiling of primary metabolites and volatiles (target pheromones as well as potential derivatives) (P1, P5). Phenotypic and GC-MS data will be obtained and analysed from ...
Submitter: Marko Petek
Studies: Investigation files, _S_P1_SPv10T0andT1, _S_P1_SPv10T2andT3, _S_P1_SPv1TransientExp, _S_P1_SxPAltAcTransferases, _S_P1_SxPv10vsSxP12, _S_P1_SxPv12T2, _S_P4_CoExpNetViz, _S_P4_DiNAR, _S_P4_GAtreat, _S_P4_SxP10-newG-DE, _S_P4_SxP10-oldG-DE, _S_P4_SxP1012-finalG, _S_P4_SxP12-newG-DE
Assays: _A_00_SxP_photos-phenotyping, _A_01_RNA1-RNAisol, _A_01_SxP_Data_Only-CoExp, _A_01_SxPv12_fastq-QC, _A_01_mapping-CLC, _A_01_toNewGenome-CLC-mapping, _A_02_FastQC-bioinfo, _A_02_Nb_datasets-CoExp, _A_02_SxPv12_mapping-CLC, _A_02_limmavoomDE-R, _A_02a_limmavoom-multim-R, _A_02a_limmavoomDEbylines-R, _A_02b_limmavoom-uniquem-R, _A_03_MapMan-visualisation, _A_03_NewGenome-MapMan, _A_03_SxPv12_limmavoom_DE-R, _A_03_mapping-CLC, _A_03a_mapping2-STAR, _A_04_GSEA-Stat, _A_04_MapManBINenrich-GSEA, _A_04_Mercator-bioinfo, _A_04_SxPv12_GeneSetEnrichment-RNAseg-GSEA, _A_05_DEstat-R, _A_05_Phenotype_analysis-Stat, _A_05_VOCcomp-Bioinfo, _A_05a_DEstat2-R, _A_05b_DElow-wt-R, _A_06_MapMan-bioinfo, _A_06_SxPv1-0_Illumina-Centrifuge, _A_07_NbAUSv1-0-InterPro, _A_07_transgenes-CLC, _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_LeavesSxPv10vsv12-GCMS, _A_P4_v10v12-phenotyping, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _A_RootsSxPv10vsv12-GCMS, _A_SP10T0Analysis-GCMS, _A_SP10T1Analysis-GCMS, _A_SPv10EaDActAnalysis-GCMS, _A_SPv10T2Analysis-GCMS, _A_SPv10T3Analysis-GCMS, _A_SPv10_phenotyping-Images, _A_SxPAlternativeAcetyltransferases-GCMS, _A_SxPv10vsv12-phenotyping, _A_SxPv12ScreeningT2-GCMS, _A_TransientSPv11andSPv12-GCMS, _I_T21_SXPsysbio-files, _S_P1_SPv10T0andT1-files, _S_P1_SPv10T2andT3-files, _S_P1_SPv1TransientExp-files, _S_P1_SxPAltAcTransferases-files, _S_P1_SxPv10vsSxP12-files, _S_P1_SxPv12T2-files, _S_P4_CoExpNetViz-files, _S_P4_DiNAR-files, _S_P4_GAtreat-files, _S_P4_SxP10-newG-DE-files, _S_P4_SxP10-oldG-DE-files, _S_P4_SxP1012-finalG-files, _S_P4_SxP12-newG-DE-files
Short Name: DiNAR Title: DiNAR analyses of SxP DE data Description: DiNAR visualisation of SxPv1.0 and SxPv1.2 expressoin data in either PIS or CKN networks. Raw Data: Principal investigator: Ĺ pela Baebler License: Creative Commons Attribution 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Marko Petek
Investigation: _I_T21_SXPsysbio
Assays: _A_CKN-DiNAR, _A_CKN_NbL35-DiNAR, _A_PIS-DiNAR, _A_PIS-SxPv12-DiNAR, _A_PIS_NbL35-DiNAR, _S_P4_DiNAR-files
Short Name: PIS-DiNAR Assay Class: DRY Assay Type: DiNAR Title: SxP v1.0 DE genes visualised in DiNAR Description: Visualisation of DE genes from SxPv1.0 data in PIS network. Mapping to genome v1, contrasts by lines (low1, low2, high1, high2) pISA Assay creation date: 2020-12-15 pISA Assay creator: Mojca Juteršek Phenodata: None Featuredata: Data:
Submitter: Marko Petek
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_T21_SXPsysbio
Study: _S_P4_DiNAR
