iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,iSyTE ,Proteomic,profiling,retina,retinal,pigment,epithelium,combined,embryonic,tissue,facilitate,ocular,disease,gene,discovery,expedite,gene,discovery,eye,development,associated,defects,,previously,developed,bioinformatics,resource-tool,iSyTE,,integrated,Systems,Tool,Eye,gene,discovery,,However,,iSyTE,presently,limited,lens,tissue,predominantly,based,transcriptomics,datasets,Therefore,,extend,iSyTE,eye,tissues,proteome,level,,performed,high-throughput,tandem,mass,spectrometry,,MS/MS,,mouse,embryonic,day,,E,14.5,retina,retinal,pigment,epithelium,combined,tissue,identified,average,3300,proteins,per,sample,,n = 5,,High-throughput,expression,profiling-based,gene,discovery,approaches-involving,either,transcriptomics,proteomics-pose,key,challenge,prioritizing,candidates,thousands,RNA/proteins,expressed,address,,used,MS/MS,proteome,data,mouse,whole,embryonic,body,,WB,,reference,dataset,performed,comparative,analysis-termed,"in,silico,WB-subtraction"-with,retina,proteome,dataset,silico,WB-subtraction,identified,90,high-priority,proteins,retina-enriched,expression,stringency,criteria,of ≥ 2.5,average,spectral,counts, ≥ 2.0,fold-enrichment,,false,discovery,rate < 0.01,top,candidates,represent,pool,retina-enriched,proteins,,several,associated,retinal,biology,and/or,defects,,e.g.,,Aldh1a1,,Ank2,,Ank3,,Dcn,,Dync2h1,,Egfr,,Ephb2,,Fbln5,,Fbn2,,Hras,,Igf2bp1,,Msi1,,Rbp1,,Rlbp1,,Tenm3,,Yap1,,etc.,,,indicating,effectiveness,approach,Importantly,,silico,WB-subtraction,also,identified,several,new,high-priority,candidates,potential,regulatory,function,retina,development,Finally,,proteins,exhibiting,expression,enriched-expression,retina,made,accessible,user-friendly,manner,iSyTE,,,https://research.bioinformatics.udel.edu/iSyTE/,,,,allow,effective,visualization,information,facilitate,eye,gene,discovery.<br>Proteomic,profiling,retina,retinal,pigment,epithelium,combined,embryonic,tissue,facilitate,ocular,disease,gene,discovery,expedite,gene,discovery,eye,development,associated,defects,,previously,developed,bioinformatics,resource-tool,iSyTE,,integrated,Systems,Tool,Eye,gene,discovery,,However,,iSyTE,presently,limited,lens,tissue,predominantly,based,transcriptomics,datasets,Therefore,,extend,iSyTE,eye,tissues,proteome,level,,performed,high-throughput,tandem,mass,spectrometry,,MS/MS,,mouse,embryonic,day,,E,14.5,retina,retinal,pigment,epithelium,combined,tissue,identified,average,3,300,proteins,per,sample,,n=5,,High-throughput,expression,profiling-based,gene,discovery,approaches-involving,either,transcriptomics,proteomics-pose,key,challenge,prioritizing,candidates,thousands,RNA/proteins,expressed,address,,used,MS/MS,proteome,data,mouse,whole,embryonic,body,,WB,,reference,dataset,performed,comparative,analysis-termed,"in,silico,WB-subtraction"-with,retina,proteome,dataset,silico,WB-subtraction,identified,90,high-priority,proteins,retina-enriched,expression,stringency,criteria,³2.5,average,spectral,counts,,³2.0,fold-enrichment,,False,Discovery,Rate,<0.01,top,candidates,represent,pool,retina-enriched,proteins,,several,associated,retinal,biology,and/or,defects,,e.g.,,Aldh1a1,,Ank2,,Ank3,,Dcn,,Dync2h1,,Egfr,,Ephb2,,Fbln5,,Fbn2,,Hras,,Igf2bp1,,Msi1,,Rbp1,,Rlbp1,,Tenm3,,Yap1,,etc.,,,indicating,effectiveness,approach,Importantly,,silico,WB-subtraction,also,identified,several,new,high-priority,candidates,potential,regulatory,function,retina,development,Finally,,proteins,exhibiting,expression,enriched-expression,retina,made,accessible,user-friendly,manner,iSyTE,,https://research.bioinformatics.udel.edu/iSyTE/,,,allow,effective,visualization,information,facilitate,eye,gene,discovery.<br>Lens,Regeneration:,Application,iSyTE,Silico,Approaches,Evaluate,Gene,Expression,Lens,Organoids,Several,protocols,established,generation,lens,organoids,embryonic,stem,cells,,ESCs,,,induced,pluripotent,stem,cells,,iPSCs,,,cells,regenerative,potential,humans,various,animal,models,important,examine,well,regenerated,lens,organoids,reflect,lens,biology,,terms,development,,homeostasis,,aging,Toward,goal,,iSyTE,database,,integrated,Systems,Tool,Eye,gene,discovery;,https://research.bioinformatics.udel.edu/iSyTE/,,,,bioinformatics,resource,tool,contains,meta-analyzed,gene,expression,data,wild-type,lens,across,different,embryonic,,postnatal,,adult,stages,,can,serve,resource,comparative,analysis,article,outlines,approaches,toward,effective,use,iSyTE,gain,insights,normal,gene,expression,mouse,lens,,enriched,expression,lens,,differential,gene,expression,select,mouse,gene-perturbation,cataract/lens,defects,models,,turn,can,used,evaluate,expression,key,lens-relevant,genes,lens,organoids,transcriptomics,,e.g.,,RNA-sequencing,,RNA-seq,,,microarrays,,etc.,,downstream,methods,,e.g.,,RT-qPCR,,etc.,.<br>,Proteomic,profiling,retina,retinal,pigment,epithelium,combined,embryonic,tissue,facilitate,ocular,disease,gene,discovery,expedite,gene,discovery,eye,development,associated,defects,,previously,developed,bioinformatics,resource-tool,iSyTE,,integrated,Systems,Tool,Eye,gene,discovery,,However,,iSyTE,presently,limited,lens,tissue,predominantly,based,transcriptomics,datasets,Therefore,,extend,iSyTE,eye,tissues,proteome,level,,performed,high-throughput,tandem,mass,spectrometry,,MS/MS,,mouse,embryonic,day,,E,14.5,retina,retinal,pigment,epithelium,combined,tissue,identified,average,3300,proteins,per,sample,,n = 5,,High-throughput,expression,profiling-based,gene,discovery,approaches-involving,either,transcriptomics,proteomics-pose,key,challenge,prioritizing,candidates,thousands,RNA/proteins,expressed,address,,used,MS/MS,proteome,data,mouse,whole,embryonic,body,,WB,,reference,dataset,performed,comparative,analysis-termed,"in,silico,WB-subtraction"-with,retina,proteome,dataset,silico,WB-subtraction,identified,90,high-priority,proteins,retina-enriched,expression,stringency,criteria,of ≥ 2.5,average,spectral,counts, ≥ 2.0,fold-enrichment,,false,discovery,rate < 0.01,top,candidates,represent,pool,retina-enriched,proteins,,several,associated,retinal,biology,and/or,defects,,e.g.,,Aldh1a1,,Ank2,,Ank3,,Dcn,,Dync2h1,,Egfr,,Ephb2,,Fbln5,,Fbn2,,Hras,,Igf2bp1,,Msi1,,Rbp1,,Rlbp1,,Tenm3,,Yap1,,etc.,,,indicating,effectiveness,approach,Importantly,,silico,WB-subtraction,also,identified,several,new,high-priority,candidates,potential,regulatory,function,retina,development,Finally,,proteins,exhibiting,expression,enriched-expression,retina,made,accessible,user-friendly,manner,iSyTE,,,https://research.bioinformatics.udel.edu/iSyTE/,,,,allow,effective,visualization,information,facilitate,eye,gene,discovery.<br>Proteomic,profiling,retina,retinal,pigment,epithelium,combined,embryonic,tissue,facilitate,ocular,disease,gene,discovery,expedite,gene,discovery,eye,development,associated,defects,,previously,developed,bioinformatics,resource-tool,iSyTE,,integrated,Systems,Tool,Eye,gene,discovery,,However,,iSyTE,presently,limited,lens,tissue,predominantly,based,transcriptomics,datasets,Therefore,,extend,iSyTE,eye,tissues,proteome,level,,performed,high-throughput,tandem,mass,spectrometry,,MS/MS,,mouse,embryonic,day,,E,14.5,retina,retinal,pigment,epithelium,combined,tissue,identified,average,3,300,proteins,per,sample,,n=5,,High-throughput,expression,profiling-based,gene,discovery,approaches-involving,either,transcriptomics,proteomics-pose,key,challenge,prioritizing,candidates,thousands,RNA/proteins,expressed,address,,used,MS/MS,proteome,data,mouse,whole,embryonic,body,,WB,,reference,dataset,performed,comparative,analysis-termed,"in,silico,WB-subtraction"-with,retina,proteome,dataset,silico,WB-subtraction,identified,90,high-priority,proteins,retina-enriched,expression,stringency,criteria,³2.5,average,spectral,counts,,³2.0,fold-enrichment,,False,Discovery,Rate,<0.01,top,candidates,represent,pool,retina-enriched,proteins,,several,associated,retinal,biology,and/or,defects,,e.g.,,Aldh1a1,,Ank2,,Ank3,,Dcn,,Dync2h1,,Egfr,,Ephb2,,Fbln5,,Fbn2,,Hras,,Igf2bp1,,Msi1,,Rbp1,,Rlbp1,,Tenm3,,Yap1,,etc.,,,indicating,effectiveness,approach,Importantly,,silico,WB-subtraction,also,identified,several,new,high-priority,candidates,potential,regulatory,function,retina,development,Finally,,proteins,exhibiting,expression,enriched-expression,retina,made,accessible,user-friendly,manner,iSyTE,,https://research.bioinformatics.udel.edu/iSyTE/,,,allow,effective,visualization,information,facilitate,eye,gene,discovery.<br>Lens,Regeneration:,Application,iSyTE,Silico,Approaches,Evaluate,Gene,Expression,Lens,Organoids,Several,protocols,established,generation,lens,organoids,embryonic,stem,cells,,ESCs,,,induced,pluripotent,stem,cells,,iPSCs,,,cells,regenerative,potential,humans,various,animal,models,important,examine,well,regenerated,lens,organoids,reflect,lens,biology,,terms,development,,homeostasis,,aging,Toward,goal,,iSyTE,database,,integrated,Systems,Tool,Eye,gene,discovery;,https://research.bioinformatics.udel.edu/iSyTE/,,,,bioinformatics,resource,tool,contains,meta-analyzed,gene,expression,data,wild-type,lens,across,different,embryonic,,postnatal,,adult,stages,,can,serve,resource,comparative,analysis,article,outlines,approaches,toward,effective,use,iSyTE,gain,insights,normal,gene,expression,mouse,lens,,enriched,expression,lens,,differential,gene,expression,select,mouse,gene-perturbation,cataract/lens,defects,models,,turn,can,used,evaluate,expression,key,lens-relevant,genes,lens,organoids,transcriptomics,,e.g.,,RNA-sequencing,,RNA-seq,,,microarrays,,etc.,,downstream,methods,,e.g.,,RT-qPCR,,etc.,.<br>