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 Rv2135c/-:

update plot	correlation	link to info on gene
Rv2904c/rplS	(cc=0.6217)	info on Rv2904c/rplS
Rv2051c/ppm1	(cc=0.558)	info on Rv2051c/ppm1
Rv0736/rslA	(cc=0.5513)	info on Rv0736/rslA
Rv2869c/rip	(cc=0.5271)	info on Rv2869c/rip
Rv2603c/-	(cc=0.4946)	info on Rv2603c/-
Rv0410c/pknG	(cc=0.4935)	info on Rv0410c/pknG
Rv0324/-	(cc=0.4924)	info on Rv0324/-
Rv3715c/recR	(cc=0.4668)	info on Rv3715c/recR
Rv3245c/mtrB	(cc=0.466)	info on Rv3245c/mtrB
Rv2241/aceE	(cc=0.4644)	info on Rv2241/aceE

Correlation of Rv2135c/- with Rv0410c/pknG

Normalized LFCs for Rv2135c/-:
(description and provenance of datasets)

	Rv2135c/-	Rv0410c/pknG
Fe_supp_jason_reseq	2.559	0.598
low_pH_jason_reseq	-0.634	0.0
NO_jason_reseq	-0.995	0.0
B6_jason_reseq	-0.421	0.0
MHCII_jason_reseq	-0.37	0.0
Isoniazid02	-2.187	-0.201
Rifampicin4	-0.49	-0.374
Ethambutol3	2.38	-0.168
Meropenem3	-0.399	-0.165
Vancomycin16	0.424	-0.366
Rv2680_day32	0.0	-0.459
H37Rv_KO_MarP	-3.718	-3.779
hypoxia_3wks	-1.511	0.0
hypoxia_6wks	-0.791	0.0
glycerol	1.758	0.0
cholesterol	0.0	0.0
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	0.127
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	2.382	1.157
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
DS0c	0.0	0.217
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	0.0	0.241
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.099	0.0
H37Rv_KO_MbtN	0.196	0.283
Trans05	0.0	0.0
macrophage_unactivated	-0.761	0.0
IL1	-1.124	0.0
Rapamycin	-1.163	0.0
Tcell	-1.235	0.0
GMCSF	-1.001	0.0
IFNab	0.0	0.0
IFNg	-1.013	0.0
IFNg_GMCSF1	-1.191	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	4.169	0.167
delta_Rv3594	-1.158	0.0
delta_Rv3717	-2.555	0.0
delta_Rv3811	-2.149	0.0
delta_Rv0954	1.49	0.876
PonA1	2.001	4.022
EccD1_KO	-2.375	-0.865
EspI_KO	-2.059	-1.275
PE35_KO	0.067	2.774
PPE68_KO	0.889	2.627
glycerol2	-0.82	0.0
lignocerate	-1.033	0.0
oleate	-1.202	0.0
phosphatidylcholine	-1.188	0.0
acetate	0.69	0.229
glucAc	0.229	0.0
Rv0950ko	1.658	-0.739
Rv1096ko	0.344	0.389
Rv3684ko	1.346	1.611
delta_otsA_trehalose	1.021	-0.133