TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv2400c/subI:

update plot	correlation	link to info on gene
Rv2399c/cysT	(cc=0.8778)	info on Rv2399c/cysT
Rv2397c/cysA1	(cc=0.8728)	info on Rv2397c/cysA1
Rv2256c/-	(cc=0.7703)	info on Rv2256c/-
Rv2198c/mmpS3	(cc=0.7277)	info on Rv2198c/mmpS3
Rv3035/-	(cc=0.6908)	info on Rv3035/-
Rv2221c/glnE	(cc=0.659)	info on Rv2221c/glnE
Rv1340/rphA	(cc=0.6558)	info on Rv1340/rphA
Rv3044/fecB	(cc=0.6529)	info on Rv3044/fecB
Rv2246/kasB	(cc=0.6236)	info on Rv2246/kasB
Rv3410c/guaB3	(cc=0.5853)	info on Rv3410c/guaB3

Correlation of Rv2400c/subI with Rv2198c/mmpS3

Normalized LFCs for Rv2400c/subI:
(description and provenance of datasets)

	Rv2400c/subI	Rv2198c/mmpS3
Fe_supp_jason_reseq	0.766	1.897
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-1.072	0.469
Rifampicin4	-1.681	-0.712
Ethambutol3	-0.755	-0.153
Meropenem3	-1.033	-0.315
Vancomycin16	-1.647	-0.698
Rv2680_day32	0.0	-0.33
H37Rv_KO_MarP	-1.307	-6.0
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	-0.209
glycerol	0.0	0.709
cholesterol	0.0	0.145
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.135
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.285	1.492
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.533
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.162
H37Rv_KO_CtpD	0.127	0.241
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.348
H37Rv_KO_MbtN	0.0	0.362
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.218	0.0
secA2_input	-2.069	-0.456
delta_Rv3594	0.211	1.937
delta_Rv3717	0.0	0.532
delta_Rv3811	0.0	0.376
delta_Rv0954	1.383	0.152
PonA1	0.884	0.566
EccD1_KO	-5.825	-4.654
EspI_KO	-6.0	-4.954
PE35_KO	2.333	0.204
PPE68_KO	-0.595	-1.177
glycerol2	0.0	-0.369
lignocerate	0.0	-0.153
oleate	0.0	-0.373
phosphatidylcholine	0.0	-0.368
acetate	0.229	2.352
glucAc	0.0	-0.272
Rv0950ko	-3.585	-2.044
Rv1096ko	-3.673	-6.0
Rv3684ko	-3.799	-0.305
delta_otsA_trehalose	1.223	-0.4