Reference:
Welcome to SalComMac, the HintonLab
Salmonella enterica serovar Typhimurium Gene Expression Compendium
(an extension of SalCom, with in vitro & intra-macrophage expression profiles)
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).
*To start:  enter query or select Examples: ssaGSTM4509prgH,ssaG,mgtCmotility genesSPI1SPI2SPI1 & 2 effectors
SPI3SPI4SPI5SPI6SPI9SPI11SPI12 + oaf O-antigen locusSPI13SPI14SPI16sRNAs
Top 100 up- and down-regulated genes in knock-out mutants:
ΔdamΔhilAΔhilCΔhilDΔhilEΔhilD ESPΔbarA/SirAΔfliZΔfurΔhfqΔrpoEΔrpoSΔhilD InSPI2ΔphoB/RΔphoP/QΔompR/EnvZΔslyAΔssrAΔssrBΔssrA/B
macrophage-induced

Heatmap for ssaG expression in strain 4/74 (Srikumar et al., 2015)

Absolute Expression Levels (transcripts per million)

query
EEP
MEP
LEP
ESP
LSP
25°C
Cold shock (15°C)
pH3 shock
pH5.8 shock
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
NonSPI2
InSPI2
InSPI2 LowMg2+
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
Macrophage
     Common gene name Gene Synonym Type Start position (4/74) End position (4/74) Strand Product (EMBL DB) LT2 ID 4-74 ID SL1344 Locus ID
ssaG  6 4 9 80 13   3   4 4 4 6 4 7 6   12 10   10 3,395 3,586 1,059 626   2,410    ssaG CDS 1446389 1446604 + Type III secretion system apparatusSTM1406 STM474_1412 SL1344_1340

coverage legend

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

Relative Expression Levels (fold-change)

query
EEP
MEP
LEP
ESP
LSP
MEP
Cold shock (15°C)
pH3 shock
pH5.8 shock
NaCl shock
Bile shock
Low Fe2+ shock
Anaerobic shock
Anaerobic growth
Oxygen shock
InSPI2
InSPI2 LowMg2+
Peroxide shock (InSPI2)
Nitric oxide shock (InSPI2)
NonSPI2
InSPI2
ESP
Macrophage
     Common gene name Gene Synonym Type Start position (4/74) End position (4/74) Strand Product (EMBL DB) LT2 ID 4-74 ID SL1344 Locus ID
ssaG  1 1 1 7.98 1.31   1 1 1 1 1 1 1 1   1 0.87   1 1.06 0.31 0.18   1 334.98   1 30.22    ssaG CDS 1446389 1446604 + Type III secretion system apparatusSTM1406 STM474_1412 SL1344_1340

ratio legend

download data:download data as tab-delimited text file

Protocols for Suite of 22 environmental conditions: Excel file, 408KB


Results provided by the Hinton Lab, automatically generated on Thu Dec 14 02:05:56 2017
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.