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 Rv2542/-:

update plot	correlation	link to info on gene
Rv2915c/-	(cc=0.4718)	info on Rv2915c/-
Rv0517/-	(cc=0.4411)	info on Rv0517/-
Rv2226/-	(cc=0.4188)	info on Rv2226/-
Rv3129/-	(cc=0.4055)	info on Rv3129/-
Rv2322c/rocD1	(cc=0.4048)	info on Rv2322c/rocD1
Rv2306B/-	(cc=0.402)	info on Rv2306B/-
Rv0406c/-	(cc=0.4001)	info on Rv0406c/-
Rv1250/-	(cc=0.3984)	info on Rv1250/-
Rv0895/-	(cc=0.3963)	info on Rv0895/-
Rv0265c/-	(cc=0.3953)	info on Rv0265c/-

Correlation of Rv2542/- with Rv3129/-

Normalized LFCs for Rv2542/-:
(description and provenance of datasets)

	Rv2542/-	Rv3129/-
Fe_supp_jason_reseq	0.513	0.144
low_pH_jason_reseq	-0.82	-0.162
NO_jason_reseq	-0.257	0.0
B6_jason_reseq	-0.109	0.925
MHCII_jason_reseq	0.142	2.625
Isoniazid02	-0.195	4.243
Rifampicin4	0.273	-1.427
Ethambutol3	-0.235	-0.882
Meropenem3	0.283	-4.097
Vancomycin16	-0.093	-1.425
Rv2680_day32	0.538	1.627
H37Rv_KO_MarP	0.082	-0.752
hypoxia_3wks	1.049	1.172
hypoxia_6wks	0.973	1.157
glycerol	-0.253	0.607
cholesterol	-0.129	0.665
AJ	-0.146	-0.472
Bibs02	0.166	-0.898
Bibs02c	0.74	0.762
BL6	-0.006	-1.212
BL6a	0.415	0.924
BXD01	-0.333	-2.722
BXD010	-0.075	0.0
BXD011	-0.126	-1.306
BXD03	-0.761	-0.664
BXD04	-0.518	-1.965
BXD05	-0.499	-2.354
BXD06	-0.007	-2.056
BXD07	-0.768	-2.686
BXD08	-0.365	-0.219
BXD09	-0.089	-1.81
CAST	-0.145	-0.829
CCcont	-0.303	-1.575
DS01	-0.115	2.933
DS02	0.805	3.266
DS04	1.072	0.294
DS0c	0.041	1.241
GP01	-1.345	-2.063
GP02	-0.852	-1.967
GP0c	-0.191	-0.942
NOD	-0.153	-1.064
NZO	-0.967	-0.134
PWK	0.161	-1.337
H37Rv_KO_CtpC	0.229	-1.975
H37Rv_KO_CtpD	-0.567	0.978
H37Rv_KO_Rv1272	-0.59	-3.334
H37Rv_KO_SugABC	0.65	-1.624
H37Rv_KO_MbtN	-0.476	-2.154
Trans05	-0.663	-2.629
macrophage_unactivated	-0.439	0.082
IL1	0.193	-0.685
Rapamycin	0.47	0.611
Tcell	0.166	0.254
GMCSF	-0.119	-1.238
IFNab	0.0	-0.892
IFNg	0.174	2.812
IFNg_GMCSF1	0.0	-0.349
Rv1432_day32	0.648	1.447
Rv1565c_day32	-0.093	0.218
secA2_input	0.775	-0.955
delta_Rv3594	-0.786	-0.176
delta_Rv3717	-0.122	-2.766
delta_Rv3811	-0.348	0.995
delta_Rv0954	-0.053	-3.489
PonA1	-0.518	-0.437
EccD1_KO	0.589	2.46
EspI_KO	0.511	1.777
PE35_KO	0.405	1.978
PPE68_KO	0.614	1.683
glycerol2	-0.021	-0.694
lignocerate	-0.074	-1.275
oleate	-0.176	0.32
phosphatidylcholine	-0.053	-0.989
acetate	-0.554	-0.795
glucAc	-0.136	-2.449
Rv0950ko	0.944	0.793
Rv1096ko	-0.021	1.954
Rv3684ko	0.164	1.647
delta_otsA_trehalose	-0.109	-0.328