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 Rv3410c/guaB3

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

	Rv2400c/subI	Rv3410c/guaB3
Fe_supp_jason_reseq	0.766	0.0
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	1.723
Rifampicin4	-1.681	0.0
Ethambutol3	-0.755	1.294
Meropenem3	-1.033	-0.165
Vancomycin16	-1.647	-0.366
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.307	-0.631
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.972
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	0.0
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	0.149
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
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	0.0
H37Rv_KO_CtpD	0.127	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	0.103
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	0.348
delta_Rv3594	0.211	0.211
delta_Rv3717	0.0	0.0
delta_Rv3811	0.0	0.0
delta_Rv0954	1.383	0.178
PonA1	0.884	0.0
EccD1_KO	-5.825	-0.793
EspI_KO	-6.0	-1.081
PE35_KO	2.333	0.601
PPE68_KO	-0.595	0.0
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.229	0.0
glucAc	0.0	0.0
Rv0950ko	-3.585	-2.31
Rv1096ko	-3.673	-1.894
Rv3684ko	-3.799	-2.057
delta_otsA_trehalose	1.223	-0.965