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EcoMap

Gene Set Overlap Query

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Proteomics:
Membrane Proteome Inner Membrane Proteome 807 IMemProt-C IN(Exp) 395 IMemProt-C OUT(Exp) 119 IMemProt-C IN(Pred) 85 IMemProt-C OUT(Pred) 14 IMemProt Pred 124 IMem_Loc_2DMS 78 LipoProteome 119 Verified Lipoproteins 82 Predicted Lipoproteins 37 Outer Membrane Proteome FimD Usher Family Paralogs 11 Mem_Loc_2DMS 28 MemProtExpress 120 MemProtEx-Minus 26 MemProtEx-Plus 91 MemProtEx-Both 33 MemProtEx-VivoOnly 18 MemProtEx-VitroOnly 40 MemProtEx-VivoStrong 15 MemProtEx-VitroStrong 35 MemProtEx-VivoWeak 36 MemProtEx-VitroWeak 38	Protein-protein Interactions Proteome Chips Proteome Chips: Mismatch Binding 1 A:C mismatch binding 20 G:T mismatch binding 20 Abasic site:G binding 20 Abasic site:A binding 20 Abasic site:C binding 19 Abasic site:T binding 20 YbaZ-binding Proteins 20 Protein Complexes Blue Native 2D PAGE (Lasserre) Blue Native 2D PAGE (Stenberg) Doodle Cross-linked Peptides
Mass Spectrometry APEX Protein levels 449 Cisplatin Targets 29 [Pt(dien)(H2O)]2+ Targets 8 Cysteine Sulfenic Acid 23 Cross-linked Peptides	Cytoplasmic Viscosity Virtual Cytoplasm
2D PAGE Blue Native 2D PAGE (Lasserre) Blue Native 2D PAGE (Stenberg)
Genetics:
Essential Genes 290 Keio Collection Glycogen Content Mutants 65 Glycogen Excess Mutants 35 Glycogen Deficient Mutants 30 Biofilm Defective Mutants 110 Keio Mutant Validations 2 Minimal Genome Reduced Genome Minimal Gene Sets Common Core 2097 CommonCore-5 2150 HT1006 1006 Non-Core971 Non-Core 971 Core Pseudogenes 20 Synthetic Biology	Gene Expression Protein Translation tRNA 86 mRNA Codons Codon Usage Start Codons Stop Codons RNA Intergenes Intergenic Repeat Families 1 REP Elements 10 IRU Repeats 1 BOXC Repeats 1 RSA Repeats 1 TERM Repeats QUAD Repeats TRIP Repeats PAIR Repeats CRISPR Repeats 11 LDR Repeats TLR Repeats 20 JUMP Repeats PDR-A Repeats PDR-E Repeats PDR-Z Repeats RNPB Repeats 5'UTR Attenuators Riboswitches lysC 5' UTR 1 thiM 5' UTR 1 Ribosome Binding Sites Transcription Start Points flhDC 5'UTR Transcription Termination 1 Rho-independent Termination Rho-dependent Termination The Ribosome rRNA 22 Ribosomal Proteins 54 Small Ribosomal Proteins 21 Large Ribosomal proteins 33 Translation Factors 9 Initiation Factors 3 Elongation Factors 2 Release Factors 4 Mistranslation Translational Regulation Translation Frameshifting RNA Transcription RNA Polymerase Holenzyme 11 RNAP Core Enzyme 4 RNAP Sigma Factors 7 RNA Expression Microarrays Transcriptional Regulation Transcription Factors TFBS Promoters 5'UTR Attenuators Riboswitches lysC 5' UTR 1 thiM 5' UTR 1 Ribosome Binding Sites Transcription Start Points flhDC 5'UTR Regulatory Modeling Operon Known Operons Predicted Operons Predicted yeaVWX 3 Predicted yihO-U 7 Regulon Sigma 54 Regulons bEBP 13 Transcription Initiation Promoters Stalled RNAP-Promoter Complexes 2 7 Stalled Complexes 7 34 Active Assayable Promoters 34 118 Screened Promoters Transcription Elongation Transcription Termination 1 Rho-independent Termination Rho-dependent Termination
Intergenes RNA Intergenes Intergenic Repeat Families 1 REP Elements 10 IRU Repeats 1 BOXC Repeats 1 RSA Repeats 1 TERM Repeats QUAD Repeats TRIP Repeats PAIR Repeats CRISPR Repeats 11 LDR Repeats TLR Repeats 20 JUMP Repeats PDR-A Repeats PDR-E Repeats PDR-Z Repeats RNPB Repeats 5'UTR Attenuators Riboswitches lysC 5' UTR 1 thiM 5' UTR 1 Ribosome Binding Sites Transcription Start Points flhDC 5'UTR Transcription Termination 1 Rho-independent Termination Rho-dependent Termination DNA Intergenes Promoters TFBS Replication Intergenes 1 KOPS 1 Chi Sites oriC 1 TerA-F Sites 6 DatA 2 Dif 3 MigS 2	Pseudogenes 168 RNA gene-derived Pseudogenes 5 Reconstructed Pseudogenes 83 Frameshifted Pseudogenes 30 In-frame Stop Pseudogenes 30 Deletion Pseudogenes 90 5' Deletion Pseudogenes 58 3' Deletion Pseudogenes 35 Internal Deletion Pseudogenes 4 Interrupted Pseudogenes 15 Functional Pseudogenes Y-pseudogenes 115
Horizontal Gene Transfer 912 IS Elements 17 IS1 2 IS2 2 IS3 2 IS4 1 IS5 1 IS30 1 IS600 1 IS911 2 IS186 1 ISX' and ISZ' 2 IS150 2 Prophages 223 CP4-6 35 DLP12 32 e14 22 Rac 29 Qin/Kim 36 CPS-53/KpLE1 18 Eut/CPZ-55 9 CP4-57 26 CP4-44 14 PR-X 2 Genetic Transfer Transduction Conjugation Transformation HT1006 1006 HT Pseudogenes 28	EcoFam Orthologs YjhY 1 YpfM 1 YbfG 1 YbbD 1 Paralogs MscS Mechanosensitive Channels 6 Major Facilitator Permeases 84 Rhs Element Repeat-encoded Proteins 9 FimD Usher Family Paralogs 11 FimA Paralogs 25 AAA+ ATPases 120 bEBP 13
DNA Biotechnology Polymerase Chain Reaction DNA Restriction and Modification Recombineering Molecular Cloning DNA Hybridization DNA Sequencing Whole Genome Resequencing DNA Protection Assays Gel Mobility Shift Assay Expression Systems Cell-free Expression DNA Purification	DNA Repeats Intergenic Repeat Families 1 REP Elements 10 IRU Repeats 1 BOXC Repeats 1 RSA Repeats 1 TERM Repeats QUAD Repeats TRIP Repeats PAIR Repeats CRISPR Repeats 11 LDR Repeats TLR Repeats 20 JUMP Repeats PDR-A Repeats PDR-E Repeats PDR-Z Repeats RNPB Repeats Microsatellites (SSRs) 3
Annotation Science Experimental Verification Verification of Activity Verification of Start and Stop Verified Set Verification of Expression Verified Set Verification of Mutation and Phenotype Verification of Protein Localization Verified Set Predictive Annotation Comparative Genomics and Homology Analysis Functional Predictions using Homology Gene or Feature Interval Predictions u