EcoGene
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Gene Set Overlap Query
Proteomics:
Protein-protein Interactions (PPI)
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)
SubProteomes
Periplasmic Proteome
Extracellular Proteome
63
Structural Genomics Projects
Structure2Function Project
111
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
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
AraC Transcriptional Activator Family
28
5'UTR
Attenuators
Riboswitches
lysC 5' UTR
1
thiM 5' UTR
1
moaA 5' UTR
1
thiB 5' UTR
1
Ribosome Binding Sites
Transcription Start Points
flhDC 5'UTR
Long 5' UTRs
gadE 5' UTR
1
Short 5' UTRs
tauA 5' UTR
1
Regulatory Modeling
cAMP Input Functions
19
Operon
Known Operons
Predicted Operons
Predicted
yeaVWX
3
Predicted
yihO-U
7
Regulon
Sigma 54 Regulons
bEBP
13
cAMP Input Functions
19
Predicted Regulons McCue 2002
219
Nitrogen regulated (Ntr) response
Transcription Initiation
Promoters
Curved Promoters
225
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
Chromosome Metabolism
1
DNA Replication
DNA Polymerases
14
DNA Repair
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
DNA Polymerases
14
DNA Recombination
DNA Restriction and Modification
Intergenes
RNA Intergenes
Intergenic Repeat Families
REP Elements
4
IRU Repeats
BOXC Repeats
RSA Repeats
TERM Repeats
SIB Repeats
TRIP Repeats
PAIR Repeats
CRISPR Repeats
10
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
moaA 5' UTR
1
thiB 5' UTR
1
Ribosome Binding Sites
Transcription Start Points
flhDC 5'UTR
Long 5' UTRs
gadE 5' UTR
1
Short 5' UTRs
tauA 5' UTR
1
Transcription Termination
1
Rho-independent Termination
Rho-dependent Termination
DNA Intergenes
Promoters
Curved Promoters
225
TFBS
Replication Intergenes
1
KOPS
1
Chi Sites
oriC
1
Ter and pTer Sites
14
DatA
2
Dif
3
MigS
2
Regions of Extreme Structure
20
Pseudogenes
175
RNA gene-derived Pseudogenes
5
Reconstructed Pseudogenes
84
Frameshifted Pseudogenes
31
In-frame Stop Pseudogenes
30
Deletion Pseudogenes
95
5' Deletion Pseudogenes
59
3' Deletion Pseudogenes
36
Internal Deletion Pseudogenes
5
Interrupted Pseudogenes
15
Functional Pseudogenes
Y-pseudogenes
116
Horizontal Gene Transfer
911
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
224
CP4-6
35
DLP12
32
e14
23
Rac
29
Qin/Kim
37
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
YfdP
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
ABC transporter ATPases
75
AraC Transcriptional Activator Family
28
Rhodanese domain proteins
8
L,D-transpeptidases
5
Nucleobase permeases
10
ABC transporter ATPases
75
Outer membrane factor (OMF) proteins
4
Periplasmic binding proteins
47
Periplasmic binding proteins, OppA family
9
Periplasmic binding proteins, HisJ family
10
Periplasmic binding proteins, BtuF family
4
Periplasmic binding proteins, MalE family
11
Periplasmic binding proteins, RbsB family
8
Periplasmic binding proteins, ProX family
3
Periplasmic binding proteins, ProX family
3
ABC transporter permeases, major family
50
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
GFP Reporters
DNA Repeats
Intergenic Repeat Families
REP Elements
4
IRU Repeats
BOXC Repeats
RSA Repeats
TERM Repeats
SIB Repeats
TRIP Repeats
PAIR Repeats
CRISPR Repeats
10
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 using Homology
Minimal Gene Sets
Common Core
2097
CommonCore-5
2150
HT1006
1006
Non-Core971
Non-Core
971
Core Pseudogenes
20
Phylogenetic Profiles
PanColi
PanColi strains
Intrinsic Sequence Analysis
Functional Predictions using Intrinsic Properties
Gene or Feature Interval Predictions using Intrinsic Properties
Text Mining
Systematic nomenclature
Y-genes
1523
Y-pseudogenes
116
Prophage gene mnemonics
Common Core
2097
CommonCore-5
2150
HT1006
1006
Non-Core971
Non-Core
971
Core Pseudogenes
20
Biochemistry:
Peptidases and their homologs
136
Aspartic Peptidases
7
A08 Family Peptidases
1
A24 Family Peptidases
2
A26 Family Peptidases
1
A31 Family Peptidases
3
Cysteine Peptidases
20
C26 Family Peptidases
6
C40 Family Peptidases
4
C44 Family Peptidases
5
C48 Family Peptidases
1
C56 Family Peptidases
4
Metallo Peptidases
54
M01 Family Peptidases
1
M03 Family Peptidases
2
M14 Family Peptidases
1
M15 Family Peptidases
2
M16 Family Peptidases
3
M17 Family Peptidases
2
M20 Family Peptidases
8
M22 Family Peptidases
3
M23 Family Peptidases
4
M24 Family Peptidases
4
M28 Family Peptidases
2
M38 Family Peptidases
12
M41 Family Peptidases
1
M42 Family Peptidases
3
M48 Family Peptidases
4
M50 Family Peptidases
1
M74 Family Peptidases
1
Serine Peptidases
45
S01 Family Peptidases
4
S09 Family Peptidases
9
S11 Family Peptidases
4
S12 Family Peptidases
3
S13 Family Peptidases
1
S14 Family Peptidases
1
S16 Family Peptidases
4
S24 Family Peptidases
3
S26 Family Peptidases
1
S33 Family Peptidases
9
S41 Family Peptidases
1
S49 Family Peptidases
2
S51 Family Peptidases
1
S54 Family Peptidases
1
S66 Family Peptidases
1
Threonine Peptidases
3
T01 Family Peptidases
1
T02 Family Peptidases
1
T03 Family Peptidases
1
Colony formation and morphology
Unknown Peptidases
7
U32 Family Peptidases
4
U49 Family Peptidases
1
U62 Family Peptidases
2
Protein Modifications
Oxidized Proteins
58
Oxidized Proteins, Nitrogen
34
Oxidized Proteins, Carbon
36
Oxidized Proteins, Phosphate
9
Protein Phosphorylation
Chaperones
GroESL chaperonin
GroESL substrates
Kerner GroESL substrates
Kerner Class I GroESL substrates
Kerner Class II GroESL substrates
Kerner Class III GroESL substrates
DnaJK-GrpE chaperone system
Clp Protease/Chaperones
Structural Biology
Protein Structure
Kinetically Stable Proteins
45
X-ray Crystal Structures
Structural Genomics Projects
Structure2Function Project
111
NMR Structures
Protein Dynamics
Intrinsically Disordered Proteins
Predicted IDPs
Experimental IDPs
3
Protein Folding
BBL Fast Folding
1
Protein unfolding
Heat-stable Proteins
17
Nucleic Acid Structure
RNA Structure
DNA Structure
Regions of Extreme Structure
20
Membranes
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
120
Verified Lipoproteins
82
Predicted Lipoproteins
38
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
Multicomponent Transport Systems
Major Facilitator Permeases
84
PTS Sugar Transport
Multidrug Resistance (MDR) Efflux Pumps
28
ABC (ATP-Binding Cassette) systems
ABC transporter permeases
58
ABC transporter permeases, major family
50
ABC transporter permeases, FecCD family
6
ABC transporter ATPases
75
Membrane fusion proteins
15
Outer membrane factor (OMF) proteins
4
Periplasmic binding proteins
47
Periplasmic binding proteins, OppA family
9
Periplasmic binding proteins, HisJ family
10
Periplasmic binding proteins, BtuF family
4
Periplasmic binding proteins, MalE family
11
Periplasmic binding proteins, RbsB family
8
Periplasmic binding proteins, ProX family
3
Individual ABC transporter systems
ABC importers
ThiBPQ thiamine ABC transporter
3
FhuABCD iron-ferrichrome ABC transport system
4
MetNIQ L,D-methionine ABC transpotrer
3
TauABC taurine ABC transporter
3
Defective ABC importers
AfuB'C defective ferric ABC transporter
2
ABC exporters
MdlAB multidrug ABC exporter
2
ABC transporter permease-ATPases
3
Model Membranes
Inner Membrane
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
Outer Membrane
Outer Membrane Proteome
FimD Usher Family Paralogs
11
Murein biosynthesis and degradation
Penicillin Binding Proteins
11
Murein hydrolases
21
Murein synthases
6
L,D-transpeptidases
5
Thiol Redox System
10
SecY Translocon
12
Microbiology:
Biofilms
Biofilm Competitive Fitness
190
Biofilm-Important Genes
114
Planktonic-Important Genes
76
Biofilm Defective Mutants
110
Bacterial Growth
Stress Responses
Stringent response and growth rate control
3
Growth Media
Cell division
Mouse Gut Colonization
Cyclic-di-GMP Signaling
2
Diguanylate cyclase
19
Cyclic-di-GMP phosphodiesterase
17
Dual GGDEF/EAL domain proteins
7
Cell Surface
Chemotaxis
Motility and Flagella
L-forms
Optical Tweezers
Cell Shape
Cell Adhesion
Autotransporters
14
Cell Fusion
Microinformatics
Whole Cell Modeling
E. coli Websites
RNA:
RNA Products
173
sRNA
61
rRNA
22
tRNA
86
mRNA
Codons
Codon Usage
Start Codons
Stop Codons
RNA gene-derived Pseudogenes
5
Proteins of RNA Metabolism
Ribosomal Proteins
54
Small Ribosomal Proteins
21
Large Ribosomal proteins
33
Ribonucleases
Exoribonucleases
RNA degradosome
4
Endoribonucleases
RNA Modification
RNA Methyltransferases
Pseudouridine Synthases
11
RNA Chaperones
RNA Helicases
RNA Polymerase Holenzyme
11
RNAP Core Enzyme
4
RNAP Sigma Factors
7
RNA Biotechnology
RNA End Mapping
RACE
Primer Extension
RNA Protection Assays
Transcription Start Points
flhDC 5'UTR
Northern Blots
: