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Analysis: Discovery of coregulated genes

Scenario 4. Analysis: Discovery of coregulated genes. What follows is a simulation of the proposed graphical interface. As you go through the simulation please consider what capabilities you would want to serve your research and annotation interests.

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Analysis: Discovery of coregulated genes

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  1. Scenario 4 Analysis: Discovery of coregulated genes What follows is a simulation of the proposed graphical interface. As you go through the simulation please consider what capabilities you would want to serve your research and annotation interests. A narrative to help you go through the simulation appears in a red-bordered box, such as the one below. To begin:1. Click on Slide Show, (on the upper toolbar)2. Click View Show3. Click Continue button Continue

  2. How do cells control response to light? What genes are related to the adaptation to high light? Look for: • Gene present in Prochlorococcus MED4 MED4 is naturally adapted to grow in high light. • Ortholog absent in Prochlorococcus MIT9313 MIT9313 is naturally adapted to grow in low light • Ortholog present in Synechocystis PCC 6803 Reason will become apparent in a moment • Synechocystis PCC 6803 ortholog responds to high light Gene turns on by factor > 2 in response to high light Continue

  3. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Click to start building a new set Click to see set you or someone else made Click to see statements to manipulate sets Click to give a value to a new or old variable Click to access results of experiments Click to see list of available statements Click to see list of available manipulations Click any red button to get help Build set Display set Set operation Variable Data Operation Function Click Build Set to begin finding orfs with the desired specifications

  4. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Click to see statements to manipulate sets Click to give a value to a new or old variable Click to access results of experiments Click to see list of available statements Click to see list of available manipulations Click any red button to get help Set operation Variable Data Operation Function You want to go through all MED4 ORFS. Click Operation to see how to do that.

  5. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Consider X in set... (loop) IF... THEN... OTHERWISE Consider X in set... (loop) Click to go through each element of a set Click to perform actions only under certain conditions Click any red button to get help Consider X in set... (loop) IF... THEN... OTHERWISE You want to go consider each ORF in the set of all all MED4 ORFS. Click Consider X in set…

  6. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Choose set type Choose database Consider each item in All nucleotides of All open reading frames of All amino acid sequences of All intergenic regions of Human-annotated orfs of Private set Public set Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH Synechocystis PCC 6803 Thermosynechococcus Trichodesmium Unicellulular Filamentous All All open reading frames of Choose ORFs as the set type and Prochlorococcus MED4 as the database.

  7. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Choose database Consider each item in All open reading frames of Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH Synechocystis PCC 6803 Thermosynechococcus Trichodesmium Unicellulular Filamentous All Prochlorococcus MED4 Choose ORFs as the set type and Prochlorococcus MED4 as the database.

  8. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 Click to give a value to a new or old variable Click to access results of experiments Click to see list of available statements Click to see list of available manipulations Click to see statements to manipulate sets Variable Data Operation Function Set operation You want to consider this MED4 ORF only if an ortholog in MIT9313 doesn’t exist.. Click Operation and choose If… then…

  9. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Consider X in set... (loop) IF... THEN... OTHERWISE KEEP item IF... THEN... OTHERWISE : Consider each item in All open reading frames of Prochlorococcus MED4 Click to go through each element of a set Click to perform actions only under certain conditions Click to add item to set Click any red button to get help Consider X in set... (loop) IF... THEN... OTHERWISE Keep item You want to this MED4 ORF only if an ortholog in MIT9313 doesn’t exist.. Click Operation and choose If… then…

  10. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 Click or to begin specifying condition to be met Variable Data Function IF Your condition is that the ortholog of the item in MIT9313 doesn’t exist. Ortholog of… is a function.

  11. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Ortholog of Protein product of Sequence of Upstream region of Downstream region of Ortholog of : Consider each item in All open reading frames of Prochlorococcus MED4 IF Your condition is that the ortholog of the item in MIT9313 doesn’t exist. Ortholog of… is a function.

  12. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 Variable Choose database ( in ) IF Ortholog of Item Set Specify Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 Thermosynechococcus Trichodesmium Item You want the ortholog of the item (the specific ORF of MED4 being considered)…

  13. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 Choose database ( in ) IF Ortholog of Item Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 Thermosynechococcus Trichodesmium Prochlorococcus MIT9313 ... And you want the ortholog of the item in Prochlorococcus MIT9313

  14. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done =  exists doesn’t exist : Consider each item in All open reading frames of Prochlorococcus MED4 doesn’t exist ( in ) IF Ortholog of Item Prochlorococcus MIT9313 Click specific operation to continue specifying the condition to be met or click to save results of function Variable You want the ortholog of the item in Prochlorococcus MIT9313 not to exist.

  15. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND OR BUT NOT IF... THEN... OTHERWISE : Consider each item in All open reading frames of Prochlorococcus MED4 ( in ) IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Click a logical operation to continue specifying the condition to be met or IF... THEN... to end the condition Let’s pause to see where we are in the task at hand (Click to proceed)

  16. How do cells control response to light? What genes are related to the adaptation to high light? Look for: • Gene present in Prochlorococcus MED4 MED4 is naturally adapted to grow in high light. √ • Ortholog absent in Prochlorococcus MIT9313 MIT9313 is naturally adapted to grow in low light √ • Ortholog present in Synechocystis PCC 6803 Reason will become apparent in a moment • Synechocystis PCC 6803 ortholog responds to high light Gene turns on by factor > 2 in response to high light Continue

  17. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND OR BUT NOT IF... THEN... OTHERWISE AND : Consider each item in All open reading frames of Prochlorococcus MED4 ( in ) IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Click a logical operation to continue specifying the condition to be met or IF... THEN... to end the condition There are more conditions to fulfill, so click AND.

  18. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in ) IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Click or to continue specifying condition to be met Variable Data Function Your condition now is that the ortholog of the item in Synechocystisdoes exist. Ortholog of… is a function.

  19. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Ortholog of Protein product of Sequence of Upstream region of Downstream region of Ortholog of : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in ) IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Your condition now is that the ortholog of the item in Synechocystisdoes exist. Ortholog of… is a function.

  20. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Variable Choose database ( in ) Ortholog of ItemSet Specify Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 Thermosynechococcus Trichodesmium Item You want the ortholog of the item (the specific ORF of MED4 being considered)…

  21. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 Choose database ( in ) Ortholog of Item Arthrobacter platensis Gloeobacter violaceus Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 Thermosynechococcus Trichodesmium You want the ortholog of the item in Synechocystis PCC 6803 Synechocystis PCC6803

  22. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done =  exists doesn’t exist : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) Ortholog of Item Synechocystis PCC 6803 Click specific operation to continue specifying the condition to be met or click to save results of function Variable You want the ortholog of the item in Synechocystis PCC 6803, this time to exist... but first you need to save the ortholog for later. To do this click Variable.

  23. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) Ortholog of Item Synechocystis PCC 6803 Type variable name ) (assigned to 6803 ortholog Give the ortholog a logical name so that you can refer to it later (for now, just click on the box and I’ll do the typing)

  24. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done =  exists doesn’t exist : Consider each item in All open reading frames of Prochlorococcus MED4 exists AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) Ortholog of Item Synechocystis PCC 6803 ) (assigned to 6803 ortholog Click specific operation to continue specifying the condition to be met or click to save results of function Variable Now you can demand that the ortholog of the item in Synechocystis PCC 6803 exists.

  25. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND OR BUT NOT IF... THEN... OTHERWISE AND : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog Click a logical operation to continue specifying the condition to be met or IF... THEN... to end the condition Still one more condition (2x expression) so click AND.

  26. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog Click or to continue specifying condition to be met Variable Data Function This time the condition to be met concerns data from a microarray experiment. Click Data.

  27. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog Variable Choose organism used data for in Item6803 ortholog Specify Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 6803 ortholog The data desired concerns the 6803 ortholog and an experiment using Synechocystis PCC6803

  28. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog Choose organism used data for in 6803 ortholog Microcystis aeruginosa Nostoc punctiforme Nostoc PCC 7120 Prochlorococcus MED4 Prochlorococcus MIT9313 Prochlorococcus S120 Synechococcus PCC6301 Synechococcus PCC7942 Synechococcus WH8102 Synechocystis PCC 6803 The data desired concerns the 6803 ortholog and an experiment using Synechocystis PCC6803 Synechocystis PCC 6803

  29. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog Choose type data for in 6803 ortholog Synechocystis PCC 6803 microarray 2D gel microarray It’s a microarray experiment…

  30. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists High light vs low light experiment ) (assigned to 6803 ortholog Choose expt data for in Hihara1 Suzuki1 Yoshimura1 6803 ortholog Synechocystis PCC 6803 microarray Hihara1 It’s a microarray experiment, Hihara et al, you think… Mouse over that experiment to see (here click on it)

  31. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done < < or = =  > or = > exists doesn’t exist : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 > ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray You want the experimental condition (high light) to be greater than the control…

  32. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray Value You want the experimental condition (high light) to be greater than the control by a factor of 2 (I’ll type it). > +2

  33. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND OR BUT NOT IF... THEN... OTHERWISE : Consider each item in All open reading frames of Prochlorococcus MED4 AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray Value > +2 Click a logical operation to continue specifying the condition to be met or IF... THEN... to end the condition (Let’s pause again)

  34. How do cells control response to light? What genes are related to the adaptation to high light? Look for: • Gene present in Prochlorococcus MED4 MED4 is naturally adapted to grow in high light. √ • Ortholog absent in Prochlorococcus MIT9313 MIT9313 is naturally adapted to grow in low light √ • Ortholog present in Synechocystis PCC 6803 Reason will become apparent in a moment √ • Synechocystis PCC 6803 ortholog responds to high light Gene turns on by factor > 2 in response to high light √ Continue

  35. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND OR BUT NOT IF... THEN... OTHERWISE : Consider each item in All open reading frames of Prochlorococcus MED4 IF... THEN... OTHERWISE AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray Value > That’s it! We’ve specified all the conditions, so end the IFsegment and specify what do do if all the conditions are met. +2 Click a logical operation to continue specifying the condition to be met or IF... THEN... to end the condition

  36. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 Click to give a value to a new or old variable Click to access results of experiments Click to see list of available statements Click to see list of available manipulations Click to see statements to manipulate sets Variable And if they are met, what you want to do is to save the gene in the set you’re building, a Set operation. Data Operation Function Set operation

  37. Build set Display set Set operation HELP Cancel ADD TO DELETE FROM UNION OF INTERSECTION OF Arithmetic ADD TO Variable Data Operation Function Done AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 In other words, you want to ADD the gene to the growing set.

  38. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 Variable Type name of set Add to Item6803 ortholog Specify Which gene? I could save the Prochlorococcus gene (the item), but I’ll instead save the gene from PCC 6803 (more known about them). 6803 ortholog

  39. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done AND ( in IF doesn’t exist Ortholog of Item Prochlorococcus MIT9313 ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 Type name of set Add to Light-specific genes 6803 ortholog I need to give the set a logical name (you click, I’ll type).

  40. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 Type name of set Add to Light-specific genes 6803 ortholog If I stop here, then all Prochlorococcus genes will be considered, and if the conditions are met, the 6803 ortholog will be saved. That’s what I want, so click Done. Click to give a value to a new or old variable Click to access results of experiments Click to see list of available statements Click to see list of available manipulations Click to see statements to manipulate sets Variable Data Operation Function Set operation

  41. Build set Display set Set operation HELP Cancel Variable Data Operation Function Done Save results and scriptSave only results Save results and script ( in ) AND Ortholog of Item Synechocystis PCC 6803 exists ) (assigned to 6803 ortholog data for in Hihara1 6803 ortholog Synechocystis PCC 6803 microarray THEN > +2 Type name of set Add to Light-specific genes 6803 ortholog That was a complicated script, so I’ll save it in case I (or someone else) needs to run it again or modify it.

  42. Equivalent script that bypasses interface (loop for item in (#^Genes ProcMed4) as all-orthologous = (all-blast-orthologous-geneIDsitem stdevalue) as 6803ortholog= (#^Genes Syny6803) :in all-orthologous) as light-specific-genes = nil when (and (there-are-not-any #’member-geneID-of-gene-frames (#^Genes slotv Proc9313) :in all-orthologous)) (there-are-any #'member-geneID-of-gene-frames 6803ortholog) (>= ratio-value (select-matching-geneIDs-from-table Hihara1item) 2)))) collect light-specific-genes 6803ortholog) This is the script that the interface would have produced. It looks for all the world like a computer program. In fact, it is a computer program, written in BioLingua. Continue

  43. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Here are the results of the program. The genes meeting all the conditions are given along with a brief description and a graphic display of the regions surrounding the genes. (Click to proceed)

  44. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase What can you do with this set? Certainly one thing of interest is the function of the genes. Clicking on a gene name brings you to the annotation page. Try clicking on slr1332.

  45. Main Menu Annotate Options History HELP Synechocystis PCC 6803: slr1332 Replicon: Chromosome Coordinates: 1670650 (start-ATG) 1671864 (stop)HumanLength = 404 amino acids Strand: Direct Gene name(s): fabF or fabJ Function: beta-ketoacyl-acyl carrier protein synthase Human Activity: In vivo activity: existsExperiment Cyanobacterial orthologs: A A A Syny6803 You can find out more about this kind of page from Scenarios 1 – 3. For now, click to return to the Set Display page. Nost7120 NostPun More

  46. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Another interesting point of attack is the regulation of this set of genes (after all, they were selected as being coregulated by light). Perhaps the upstream regions share a common motif. (Click to continue)

  47. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Unfortunately, in three cases, the genes don’t have an upstream region. Evidently these genes are part of operons. We’d like to consider the upstream regions of the operons by adding the first genes of the operon to the set. Add to set... that’s a Set operation. (Click on that)

  48. Build set Display set Set operation HELP Done ADD TO DELETE FROM UNION OF INTERSECTION OF Arithmetic ADD TO Operation Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Click ADD TO...

  49. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Add to set Find specific gene Add set of genes Specify gene Click on icon of gene Click ADD TO and click on the icon (the short black arrow) upstream from sll0990, the first gene without an upstream region.

  50. Build set Display set Set operation HELP Done Set: Light-specific genes Syny6803:sll0990Formaldehyde dehydrogenase (glutathione dependent) Syny6803:srl7009trnR: tRNA Arg (UCU) Syny6803:slr1332 fabFbeta ketoacyl acyl carrier protein synthase Syny6803:sll0337Sensor histidine kinase Syny6803:sll0335 Hypothetical Syny6803:sll0789 Response regulator (OmpR) Syny6803:sll0576Putative epimerase/hydratase Add to set Find specific gene Add set of genes Specify gene Click on icon of gene The short arrow is now named and part of the set. Click on the icon (the long black arrow) upstream from slr1332, the next gene without an upstream region.

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