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 Rv1016c/lpqT:

update plot	correlation	link to info on gene
Rv0170/mce1B	(cc=0.5752)	info on Rv0170/mce1B
Rv0173/lprK	(cc=0.5475)	info on Rv0173/lprK
Rv0174/mce1F	(cc=0.5249)	info on Rv0174/mce1F
Rv0169/mce1A	(cc=0.5221)	info on Rv0169/mce1A
Rv0172/mce1D	(cc=0.4956)	info on Rv0172/mce1D
Rv0167/yrbE1A	(cc=0.4854)	info on Rv0167/yrbE1A
Rv2721c/-	(cc=0.4841)	info on Rv2721c/-
Rv0171/mce1C	(cc=0.462)	info on Rv0171/mce1C
Rv2655c/-	(cc=0.4513)	info on Rv2655c/-
Rv0168/yrbE1B	(cc=0.4443)	info on Rv0168/yrbE1B

Correlation of Rv1016c/lpqT with Rv2721c/-

Normalized LFCs for Rv1016c/lpqT:
(description and provenance of datasets)

	Rv1016c/lpqT	Rv2721c/-
Fe_supp_jason_reseq	-0.751	-2.837
low_pH_jason_reseq	-0.187	-0.529
NO_jason_reseq	1.502	2.3
B6_jason_reseq	0.581	0.429
MHCII_jason_reseq	-0.292	-0.858
Isoniazid02	-0.725	1.486
Rifampicin4	1.283	2.231
Ethambutol3	1.341	-0.439
Meropenem3	1.081	2.082
Vancomycin16	0.767	-0.738
Rv2680_day32	0.81	-0.384
H37Rv_KO_MarP	0.251	-0.47
hypoxia_3wks	1.336	0.965
hypoxia_6wks	2.255	2.957
glycerol	-0.367	-0.262
cholesterol	0.544	0.358
AJ	0.324	-0.024
Bibs02	-1.325	-0.109
Bibs02c	0.618	-0.677
BL6	0.201	0.481
BL6a	1.083	0.408
BXD01	0.226	0.676
BXD010	0.884	0.875
BXD011	0.759	1.091
BXD03	-0.496	1.083
BXD04	0.704	1.654
BXD05	0.778	0.924
BXD06	0.478	1.501
BXD07	0.935	0.721
BXD08	0.251	0.778
BXD09	0.92	0.469
CAST	1.517	0.853
CCcont	0.005	-0.211
DS01	-0.183	-1.128
DS02	-0.332	-1.475
DS04	-0.337	-0.36
DS0c	0.119	-1.193
GP01	0.462	1.362
GP02	-1.26	0.963
GP0c	-0.357	1.455
NOD	0.804	0.602
NZO	0.594	0.04
PWK	0.46	1.851
H37Rv_KO_CtpC	0.232	-0.94
H37Rv_KO_CtpD	0.752	0.542
H37Rv_KO_Rv1272	0.148	-0.183
H37Rv_KO_SugABC	-0.446	0.602
H37Rv_KO_MbtN	0.15	1.345
Trans05	0.199	0.662
macrophage_unactivated	-1.001	-0.846
IL1	-1.29	-0.196
Rapamycin	-0.918	-0.516
Tcell	-1.906	-0.264
GMCSF	0.161	-0.04
IFNab	-0.284	0.339
IFNg	0.438	-0.326
IFNg_GMCSF1	-0.063	-0.434
Rv1432_day32	-0.126	-0.404
Rv1565c_day32	0.523	0.945
secA2_input	0.964	-0.128
delta_Rv3594	0.0	0.262
delta_Rv3717	0.175	0.683
delta_Rv3811	0.921	0.578
delta_Rv0954	1.054	0.066
PonA1	0.643	-0.829
EccD1_KO	0.187	-0.079
EspI_KO	-0.168	-0.277
PE35_KO	-0.225	0.114
PPE68_KO	0.573	-0.618
glycerol2	-1.041	-0.673
lignocerate	-1.24	-1.168
oleate	0.535	1.056
phosphatidylcholine	-0.634	-2.244
acetate	-0.274	-0.374
glucAc	-0.122	-0.403
Rv0950ko	0.311	0.28
Rv1096ko	-0.187	0.0
Rv3684ko	0.147	0.878
delta_otsA_trehalose	0.812	0.575