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 Rv2607/pdxH:

update plot	correlation	link to info on gene
Rv2219/-	(cc=0.5654)	info on Rv2219/-
Rv2237/-	(cc=0.543)	info on Rv2237/-
Rv1062/-	(cc=0.541)	info on Rv1062/-
Rv3208A/TB9.4	(cc=0.5368)	info on Rv3208A/TB9.4
Rv2307A/-	(cc=0.5355)	info on Rv2307A/-
Rv0042c/-	(cc=0.5271)	info on Rv0042c/-
Rv2008c/-	(cc=0.5189)	info on Rv2008c/-
Rv1987/-	(cc=0.516)	info on Rv1987/-
Rv2821c/-	(cc=0.4862)	info on Rv2821c/-
Rv2019/-	(cc=0.4818)	info on Rv2019/-

Correlation of Rv2607/pdxH with Rv2237/-

Normalized LFCs for Rv2607/pdxH:
(description and provenance of datasets)

	Rv2607/pdxH	Rv2237/-
Fe_supp_jason_reseq	0.096	0.23
low_pH_jason_reseq	-0.31	-0.676
NO_jason_reseq	-1.664	-0.302
B6_jason_reseq	-0.401	-0.548
MHCII_jason_reseq	0.581	0.053
Isoniazid02	-1.104	0.397
Rifampicin4	0.85	-0.674
Ethambutol3	-0.803	-0.32
Meropenem3	-0.355	-0.231
Vancomycin16	-0.515	-0.064
Rv2680_day32	-0.08	0.594
H37Rv_KO_MarP	-0.172	0.254
hypoxia_3wks	-0.674	-0.762
hypoxia_6wks	-0.447	-0.814
glycerol	0.513	0.12
cholesterol	0.199	0.447
AJ	0.027	0.235
Bibs02	-0.585	0.013
Bibs02c	-0.247	-0.52
BL6	0.401	0.847
BL6a	-0.468	0.201
BXD01	-0.439	-0.443
BXD010	0.284	0.241
BXD011	-0.117	0.53
BXD03	0.374	-0.725
BXD04	-0.238	-0.369
BXD05	0.776	0.165
BXD06	0.0	0.284
BXD07	-0.277	-0.399
BXD08	-0.032	-0.084
BXD09	-0.184	0.228
CAST	0.432	-0.464
CCcont	0.512	1.023
DS01	0.226	0.399
DS02	0.05	1.096
DS04	-0.191	0.45
DS0c	0.449	0.129
GP01	0.478	0.95
GP02	-0.287	-0.93
GP0c	-0.055	0.356
NOD	1.442	-0.371
NZO	0.147	0.35
PWK	0.057	-0.625
H37Rv_KO_CtpC	-0.235	-0.013
H37Rv_KO_CtpD	0.305	-0.315
H37Rv_KO_Rv1272	-0.016	-0.297
H37Rv_KO_SugABC	0.927	0.422
H37Rv_KO_MbtN	-0.33	0.656
Trans05	0.491	0.02
macrophage_unactivated	0.0	0.076
IL1	-0.596	0.24
Rapamycin	-0.715	-0.11
Tcell	-1.323	0.339
GMCSF	-0.837	-0.261
IFNab	-0.127	0.0
IFNg	-0.756	0.644
IFNg_GMCSF1	-0.968	0.628
Rv1432_day32	0.608	-0.01
Rv1565c_day32	-0.131	-0.479
secA2_input	-0.294	0.252
delta_Rv3594	1.64	1.153
delta_Rv3717	1.367	1.364
delta_Rv3811	1.48	0.772
delta_Rv0954	-0.039	0.16
PonA1	-1.272	0.84
EccD1_KO	0.194	0.53
EspI_KO	-0.057	0.91
PE35_KO	0.796	0.858
PPE68_KO	0.23	0.733
glycerol2	0.799	1.88
lignocerate	1.642	2.527
oleate	-0.54	-1.276
phosphatidylcholine	1.912	2.426
acetate	1.338	2.72
glucAc	1.263	2.503
Rv0950ko	-0.431	0.0
Rv1096ko	-0.709	-0.078
Rv3684ko	-0.675	-0.819
delta_otsA_trehalose	-0.459	-0.569