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 Rv3788/-:

update plot	correlation	link to info on gene
Rv0303/-	(cc=0.4881)	info on Rv0303/-
Rv0071/-	(cc=0.4765)	info on Rv0071/-
Rv0484c/-	(cc=0.4679)	info on Rv0484c/-
Rv1761c/-	(cc=0.428)	info on Rv1761c/-
Rv2636/-	(cc=0.4229)	info on Rv2636/-
Rv0724A/-	(cc=0.3979)	info on Rv0724A/-
Rv0918/-	(cc=0.3973)	info on Rv0918/-
Rv0483/lprQ	(cc=0.3962)	info on Rv0483/lprQ
Rv0445c/sigK	(cc=0.396)	info on Rv0445c/sigK
Rv0592/mce2D	(cc=0.3959)	info on Rv0592/mce2D

Correlation of Rv3788/- with Rv0303/-

Normalized LFCs for Rv3788/-:
(description and provenance of datasets)

	Rv3788/-	Rv0303/-
Fe_supp_jason_reseq	-0.401	0.071
low_pH_jason_reseq	-0.823	-0.577
NO_jason_reseq	-0.685	-0.494
B6_jason_reseq	-1.016	0.857
MHCII_jason_reseq	0.244	-0.077
Isoniazid02	0.227	-0.162
Rifampicin4	-0.439	-0.13
Ethambutol3	0.056	-0.206
Meropenem3	-0.158	-0.156
Vancomycin16	-1.451	-0.127
Rv2680_day32	-0.326	0.829
H37Rv_KO_MarP	0.111	0.241
hypoxia_3wks	-0.259	0.136
hypoxia_6wks	-0.263	0.66
glycerol	0.81	-0.13
cholesterol	0.463	-0.764
AJ	0.898	-0.343
Bibs02	0.069	-0.65
Bibs02c	0.17	0.853
BL6	0.246	0.246
BL6a	-0.839	0.098
BXD01	-0.732	-0.735
BXD010	-0.592	-0.357
BXD011	-0.781	-0.805
BXD03	-0.992	-0.487
BXD04	-0.7	-0.092
BXD05	-0.088	-0.316
BXD06	-0.275	-0.356
BXD07	-0.627	-0.369
BXD08	-0.877	-1.018
BXD09	-0.579	-0.325
CAST	0.35	0.317
CCcont	-0.215	-0.969
DS01	-0.051	-0.075
DS02	0.573	0.325
DS04	-0.625	0.24
DS0c	-0.02	0.239
GP01	-0.665	-0.658
GP02	-1.084	-1.356
GP0c	-0.608	-0.727
NOD	1.378	0.436
NZO	0.676	-0.376
PWK	0.318	0.159
H37Rv_KO_CtpC	0.737	-0.116
H37Rv_KO_CtpD	0.672	0.669
H37Rv_KO_Rv1272	-1.091	0.418
H37Rv_KO_SugABC	-2.448	-1.585
H37Rv_KO_MbtN	-0.968	-1.073
Trans05	-0.334	-0.511
macrophage_unactivated	-0.685	-0.177
IL1	-0.314	-0.092
Rapamycin	-0.126	-0.733
Tcell	-0.925	-0.287
GMCSF	-0.415	-0.301
IFNab	-0.381	-0.856
IFNg	0.0	-0.083
IFNg_GMCSF1	-0.952	-0.984
Rv1432_day32	0.738	0.31
Rv1565c_day32	-0.472	0.028
secA2_input	1.594	0.554
delta_Rv3594	-0.462	-0.58
delta_Rv3717	-0.344	-0.312
delta_Rv3811	-0.143	-0.739
delta_Rv0954	-0.836	-0.868
PonA1	0.507	-0.119
EccD1_KO	-0.888	-0.197
EspI_KO	-1.124	-0.836
PE35_KO	-0.613	-0.744
PPE68_KO	-1.357	-0.733
glycerol2	-0.2	-0.067
lignocerate	0.186	-0.311
oleate	0.02	0.024
phosphatidylcholine	0.253	-0.126
acetate	-0.575	-0.603
glucAc	-0.549	-0.315
Rv0950ko	0.516	0.651
Rv1096ko	-0.241	1.095
Rv3684ko	-0.452	0.956
delta_otsA_trehalose	0.734	1.464