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 Rv2960c/-:

update plot	correlation	link to info on gene
Rv1987/-	(cc=0.704)	info on Rv1987/-
Rv3208A/TB9.4	(cc=0.556)	info on Rv3208A/TB9.4
Rv3217c/-	(cc=0.5323)	info on Rv3217c/-
Rv2119/-	(cc=0.5275)	info on Rv2119/-
Rv2544/lppB	(cc=0.5174)	info on Rv2544/lppB
Rv0945/-	(cc=0.5169)	info on Rv0945/-
Rv0349/-	(cc=0.5159)	info on Rv0349/-
Rv0997/-	(cc=0.5155)	info on Rv0997/-
Rv2019/-	(cc=0.5113)	info on Rv2019/-
Rv2237/-	(cc=0.5062)	info on Rv2237/-

Correlation of Rv2960c/- with Rv1987/-

Normalized LFCs for Rv2960c/-:
(description and provenance of datasets)

	Rv2960c/-	Rv1987/-
Fe_supp_jason_reseq	1.135	0.813
low_pH_jason_reseq	-1.29	-0.965
NO_jason_reseq	-0.756	-0.761
B6_jason_reseq	1.024	0.082
MHCII_jason_reseq	0.959	-0.367
Isoniazid02	-0.287	-0.346
Rifampicin4	0.084	-0.709
Ethambutol3	1.799	-0.343
Meropenem3	-0.775	-0.765
Vancomycin16	-0.276	-0.053
Rv2680_day32	1.608	0.985
H37Rv_KO_MarP	-1.116	-0.008
hypoxia_3wks	-0.048	-1.025
hypoxia_6wks	-1.029	-0.265
glycerol	-0.835	-0.933
cholesterol	-0.459	-0.517
AJ	-0.55	-0.679
Bibs02	-1.057	0.878
Bibs02c	0.929	0.697
BL6	0.902	0.885
BL6a	0.656	0.422
BXD01	0.378	0.19
BXD010	-0.228	0.059
BXD011	0.649	0.262
BXD03	0.612	0.478
BXD04	0.777	0.068
BXD05	0.767	0.698
BXD06	-0.144	0.355
BXD07	0.97	0.167
BXD08	0.666	0.438
BXD09	0.493	0.363
CAST	-0.145	-0.289
CCcont	1.087	1.188
DS01	0.033	0.183
DS02	-0.709	-0.072
DS04	0.708	0.572
DS0c	0.225	-0.083
GP01	0.039	0.187
GP02	0.907	-0.69
GP0c	-0.082	-0.935
NOD	0.799	-0.295
NZO	-1.351	-0.767
PWK	-0.182	-0.163
H37Rv_KO_CtpC	0.692	0.154
H37Rv_KO_CtpD	0.59	1.731
H37Rv_KO_Rv1272	1.133	0.848
H37Rv_KO_SugABC	1.602	1.386
H37Rv_KO_MbtN	-0.726	-0.315
Trans05	-0.181	0.03
macrophage_unactivated	0.521	0.265
IL1	0.119	0.409
Rapamycin	-0.574	0.69
Tcell	0.215	-0.541
GMCSF	0.325	0.393
IFNab	-0.166	0.242
IFNg	0.409	0.398
IFNg_GMCSF1	1.002	0.795
Rv1432_day32	0.3	0.194
Rv1565c_day32	0.444	0.117
secA2_input	-1.262	-0.418
delta_Rv3594	0.541	1.086
delta_Rv3717	0.573	0.703
delta_Rv3811	0.677	0.747
delta_Rv0954	1.623	1.417
PonA1	0.502	-0.212
EccD1_KO	1.48	-0.615
EspI_KO	0.582	-0.331
PE35_KO	0.755	-0.079
PPE68_KO	0.998	0.214
glycerol2	1.892	2.285
lignocerate	2.72	2.814
oleate	-0.829	-1.163
phosphatidylcholine	1.982	2.129
acetate	2.555	2.72
glucAc	2.555	2.553
Rv0950ko	-1.025	0.033
Rv1096ko	0.332	-0.549
Rv3684ko	-0.108	-0.416
delta_otsA_trehalose	0.347	0.021