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 Rv0324/-

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

	Rv2135c/-	Rv0324/-
Fe_supp_jason_reseq	2.559	0.766
low_pH_jason_reseq	-0.634	-1.039
NO_jason_reseq	-0.995	0.0
B6_jason_reseq	-0.421	-0.571
MHCII_jason_reseq	-0.37	-0.503
Isoniazid02	-2.187	-2.557
Rifampicin4	-0.49	1.053
Ethambutol3	2.38	-0.325
Meropenem3	-0.399	-0.75
Vancomycin16	0.424	0.159
Rv2680_day32	0.0	-0.239
H37Rv_KO_MarP	-3.718	-1.143
hypoxia_3wks	-1.511	-0.459
hypoxia_6wks	-0.791	-1.658
glycerol	1.758	1.685
cholesterol	0.0	1.577
AJ	0.0	0.0
Bibs02	0.0	0.294
Bibs02c	0.0	-0.711
BL6	0.0	-0.154
BL6a	0.0	-0.521
BXD01	0.0	0.649
BXD010	0.0	0.0
BXD011	0.0	-0.076
BXD03	0.0	-0.695
BXD04	0.0	1.679
BXD05	0.0	-0.692
BXD06	0.0	-0.454
BXD07	0.0	-0.264
BXD08	0.0	-0.35
BXD09	0.0	-0.173
CAST	0.0	-1.185
CCcont	2.382	2.58
DS01	0.0	0.496
DS02	0.0	0.0
DS04	0.0	0.746
DS0c	0.0	1.442
GP01	0.0	-0.059
GP02	0.0	0.134
GP0c	0.0	-0.442
NOD	0.0	0.0
NZO	0.0	-1.026
PWK	0.0	-0.516
H37Rv_KO_CtpC	0.0	-0.427
H37Rv_KO_CtpD	0.0	1.907
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.099	0.926
H37Rv_KO_MbtN	0.196	-0.127
Trans05	0.0	0.0
macrophage_unactivated	-0.761	-0.537
IL1	-1.124	-2.106
Rapamycin	-1.163	-1.114
Tcell	-1.235	-1.183
GMCSF	-1.001	-0.694
IFNab	0.0	-1.418
IFNg	-1.013	-0.703
IFNg_GMCSF1	-1.191	-1.141
Rv1432_day32	0.0	-0.933
Rv1565c_day32	0.0	0.532
secA2_input	4.169	-0.639
delta_Rv3594	-1.158	-1.643
delta_Rv3717	-2.555	-1.004
delta_Rv3811	-2.149	-1.008
delta_Rv0954	1.49	1.764
PonA1	2.001	1.962
EccD1_KO	-2.375	-0.97
EspI_KO	-2.059	-0.679
PE35_KO	0.067	-1.397
PPE68_KO	0.889	-0.051
glycerol2	-0.82	-0.427
lignocerate	-1.033	-0.798
oleate	-1.202	-1.034
phosphatidylcholine	-1.188	-0.466
acetate	0.69	1.932
glucAc	0.229	1.092
Rv0950ko	1.658	-0.66
Rv1096ko	0.344	-1.366
Rv3684ko	1.346	-0.511
delta_otsA_trehalose	1.021	-0.429