Welcome to SalComD23580, the HintonLab
comparative Salmonella enterica Typhimurium Gene Expression Compendium
Columns of the Heat Maps can be sorted by value - just click on the headers
(° rotated)
Instructions:  Search by gene, locus or location (multiple entries separated by comma or space, use '*' for wild-card).
*To start:  enter query or select Example: ssaGmotility genesSPI1 genesSPI2SPI1 & 2 effectorsSPI3SPI4SPI5SPI6SPI9SPI11SPI12 + oaf O-antigen locusSPI13SPI14SPI16280 sRNAs

Heat map for ssaG expression in SL1344 and D23580

Colour legend:Salmonella Typhimurium ST4-74 Salmonella Typhimurium D23580

Absolute Expression Levels (transcripts per million)

query
EEP
MEP
LEP
ESP
LSP
25C
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
NoSPI2
InSPI2
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
Macrophage
EEP
MEP
LEP
ESP
LSP
25C
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
NoSPI2
InSPI2
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
Macrophage
    Systematic ID SL1344 Gene name SL1344 Gene_synonym SL1344 Strand SL1344 Location of Start ST4/74 Location of End ST4/74 Length (nt) in ST4/74 Type SL1344 Chromosome / Plasmid SL1344 Note SL1344 EMBL product SL1344 Genbank product SL1344 Genbank note SL1344 PubMed ID SL1344 Systematic Name D23580 Common Name D23580 Gene_synonym D23580 strand D23580 start D23580 end D23580 gene length D23580 molecule D23580 Genome Element Type D23580 Note D23580 EC D23580 GenBank Accession No. D23580 Dbid D23580 Description in Genbank D23580 LT2 orthologue 14028 orthologue ST4-74 orthologue UK-1 orthologue Alternate SL1344 identifier
ssaG  6 3 9 81 10   2   7 4 7 6   11 10   11 2,613 990 596   2,503 7 2 5 133 18   2   3 1 1 4   9 7   16 2,215 1,262 1,962   1,343 SL1344_1340 ssaG + 1446389 1446604 216 CDS chromosome Type III secretion system apparatus type III secretion system apparatus protein STMMW_14111 ssaG + 1486051 1486266 216 chromosome CDS CBG24422.1 GI:261246612 putative pathogenicity island protein STM1406 STM14_1702 STM474_1412 STMUK_1372 SL1340

coverage legend

view in JBrowse :
view SL1344 coverage data in JBrowse
  
view D23580 coverage data in JBrowse
  
download data:download data as tab-delimited text file


Intra-strain Relative Expression Levels (fold-change)

query
EEP
MEP
LEP
ESP
LSP
MEP
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
InSPI2
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
NonSPI2
InSPI2
ESP
Macrophage
EEP
MEP
LEP
ESP
LSP
MEP
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
InSPI2
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
NonSPI2
InSPI2
ESP
Macrophage
    Systematic ID SL1344 Gene name SL1344 Gene_synonym SL1344 Strand SL1344 Location of Start ST4/74 Location of End ST4/74 Length (nt) in ST4/74 Type SL1344 Chromosome / Plasmid SL1344 Note SL1344 EMBL product SL1344 Genbank product SL1344 Genbank note SL1344 PubMed ID SL1344 Systematic Name D23580 Common Name D23580 Gene_synonym D23580 strand D23580 start D23580 end D23580 gene length D23580 molecule D23580 Genome Element Type D23580 Note D23580 EC D23580 GenBank Accession No. D23580 Dbid D23580 Description in Genbank D23580 LT2 orthologue 14028 orthologue ST4-74 orthologue UK-1 orthologue Alternate SL1344 identifier
ssaG  1 1 1 8.1 1   1 1 1 1 1   1 0.9   1 0.38 0.23   1 240.2   1 30.9 1 1 1 13.34 1.79   1 1 1 1 1   1 1   1 0.57 0.89   1 136.47   1 10.07 SL1344_1340 ssaG + 1446389 1446604 216 CDS chromosome Type III secretion system apparatus type III secretion system apparatus protein STMMW_14111 ssaG + 1486051 1486266 216 chromosome CDS CBG24422.1 GI:261246612 putative pathogenicity island protein STM1406 STM14_1702 STM474_1412 STMUK_1372 SL1340

ratio legend

download data:download data as tab-delimited text file


Inter-strain Relative Expression Levels (fold-change)

query
EEP
MEP
LEP
ESP
LSP
25C
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
NoSPI2
InSPI2
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
Macrophage
    Systematic ID SL1344 Gene name SL1344 Gene_synonym SL1344 Strand SL1344 Location of Start ST4/74 Location of End ST4/74 Length (nt) in ST4/74 Type SL1344 Chromosome / Plasmid SL1344 Note SL1344 EMBL product SL1344 Genbank product SL1344 Genbank note SL1344 PubMed ID SL1344 Systematic Name D23580 Common Name D23580 Gene_synonym D23580 strand D23580 start D23580 end D23580 gene length D23580 molecule D23580 Genome Element Type D23580 Note D23580 EC D23580 GenBank Accession No. D23580 Dbid D23580 Description in Genbank D23580 LT2 orthologue 14028 orthologue ST4-74 orthologue UK-1 orthologue Alternate SL1344 identifier
ssaG  1 1 1 1.53 1.76   1   1 1 1 1   0.87 1   1.43 0.77 1.12 2.94   0.4 SL1344_1340 ssaG + 1446389 1446604 216 CDS chromosome Type III secretion system apparatus type III secretion system apparatus protein STMMW_14111 ssaG + 1486051 1486266 216 chromosome CDS CBG24422.1 GI:261246612 putative pathogenicity island protein STM1406 STM14_1702 STM474_1412 STMUK_1372 SL1340

between_strain legend

download data:download data as tab-delimited text file



Results provided by the Hinton Lab, automatically generated on Fri Jan 18 14:43:02 2019
We are very grateful to Joe Grissom and Tyrrell Conway for sharing the code that drives this compendium database, and was originally designed for use at GenExpDB.