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 Rv2113/-:

update plot	correlation	link to info on gene
Rv0159c/PE3	(cc=0.856)	info on Rv0159c/PE3
Rv1817/-	(cc=0.8479)	info on Rv1817/-
Rv3815c/-	(cc=0.7418)	info on Rv3815c/-
Rv0453/PPE11	(cc=0.7248)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7197)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.6508)	info on Rv2822c/-
Rv3685c/cyp137	(cc=0.5386)	info on Rv3685c/cyp137
Rv3862c/whiB6	(cc=0.5193)	info on Rv3862c/whiB6
Rv1021/-	(cc=0.4871)	info on Rv1021/-
Rv2339/mmpL9	(cc=0.4851)	info on Rv2339/mmpL9

Correlation of Rv2113/- with Rv2339/mmpL9

Normalized LFCs for Rv2113/-:
(description and provenance of datasets)

	Rv2113/-	Rv2339/mmpL9
Fe_supp_jason_reseq	0.922	0.283
low_pH_jason_reseq	-1.379	-0.164
NO_jason_reseq	-0.559	-0.349
B6_jason_reseq	-1.249	-0.289
MHCII_jason_reseq	-0.531	0.481
Isoniazid02	-1.043	0.375
Rifampicin4	0.406	0.0
Ethambutol3	0.657	0.568
Meropenem3	-0.462	-0.052
Vancomycin16	-0.231	0.146
Rv2680_day32	-0.825	0.365
H37Rv_KO_MarP	0.159	0.047
hypoxia_3wks	-0.012	0.267
hypoxia_6wks	-0.568	-0.177
glycerol	0.237	-0.426
cholesterol	-0.405	-0.305
AJ	0.356	0.247
Bibs02	-0.372	-0.127
Bibs02c	-0.209	-0.276
BL6	0.418	0.196
BL6a	0.169	0.211
BXD01	-0.106	0.253
BXD010	-0.113	0.557
BXD011	0.753	0.394
BXD03	0.123	0.36
BXD04	-0.166	0.565
BXD05	0.301	0.615
BXD06	0.224	0.413
BXD07	0.171	0.295
BXD08	0.265	0.087
BXD09	0.103	0.41
CAST	-0.828	0.404
CCcont	0.169	-0.197
DS01	-0.335	0.154
DS02	0.098	-0.126
DS04	-0.218	0.6
DS0c	0.11	0.578
GP01	0.072	0.591
GP02	-0.087	0.138
GP0c	0.142	0.057
NOD	-0.404	1.289
NZO	-0.604	0.35
PWK	-0.409	0.47
H37Rv_KO_CtpC	0.148	0.488
H37Rv_KO_CtpD	0.72	0.668
H37Rv_KO_Rv1272	0.551	1.099
H37Rv_KO_SugABC	1.132	0.751
H37Rv_KO_MbtN	0.42	0.571
Trans05	0.939	1.072
macrophage_unactivated	1.143	0.42
IL1	2.886	0.611
Rapamycin	3.167	0.724
Tcell	-6.0	-0.648
GMCSF	2.756	1.225
IFNab	2.663	0.801
IFNg	2.905	1.056
IFNg_GMCSF1	2.963	0.55
Rv1432_day32	0.322	0.576
Rv1565c_day32	1.531	0.3
secA2_input	0.128	-0.631
delta_Rv3594	-0.337	-0.072
delta_Rv3717	-0.154	0.0
delta_Rv3811	-0.312	0.046
delta_Rv0954	0.181	0.079
PonA1	-0.268	-0.293
EccD1_KO	0.148	-0.046
EspI_KO	0.222	-0.168
PE35_KO	-0.286	0.166
PPE68_KO	-0.147	0.355
glycerol2	0.894	0.0
lignocerate	0.616	0.339
oleate	1.331	0.081
phosphatidylcholine	0.999	0.231
acetate	0.342	-0.048
glucAc	-0.082	-0.227
Rv0950ko	0.25	0.121
Rv1096ko	-0.13	-1.095
Rv3684ko	-0.233	-0.223
delta_otsA_trehalose	0.537	-0.557