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 Rv2496c/bkdB:

update plot	correlation	link to info on gene
Rv1430/PE16	(cc=0.5391)	info on Rv1430/PE16
Rv2857c/-	(cc=0.5223)	info on Rv2857c/-
Rv0397A/-	(cc=0.5208)	info on Rv0397A/-
Rv1551/plsB1	(cc=0.508)	info on Rv1551/plsB1
Rv1021/-	(cc=0.5078)	info on Rv1021/-
Rv1353c/-	(cc=0.4926)	info on Rv1353c/-
Rv1496/-	(cc=0.4913)	info on Rv1496/-
Rv1521/fadD25	(cc=0.4806)	info on Rv1521/fadD25
Rv1729c/-	(cc=0.4775)	info on Rv1729c/-
Rv1980c/mpt64	(cc=0.4734)	info on Rv1980c/mpt64

Correlation of Rv2496c/bkdB with Rv1729c/-

Normalized LFCs for Rv2496c/bkdB:
(description and provenance of datasets)

	Rv2496c/bkdB	Rv1729c/-
Fe_supp_jason_reseq	0.469	0.158
low_pH_jason_reseq	0.381	0.673
NO_jason_reseq	1.197	0.197
B6_jason_reseq	-1.586	-0.947
MHCII_jason_reseq	0.223	-1.6
Isoniazid02	0.135	0.41
Rifampicin4	-1.21	0.103
Ethambutol3	0.22	2.122
Meropenem3	-0.789	0.45
Vancomycin16	-0.13	0.748
Rv2680_day32	-0.05	0.659
H37Rv_KO_MarP	-0.354	0.667
hypoxia_3wks	0.63	0.427
hypoxia_6wks	0.0	-0.159
glycerol	-1.463	0.686
cholesterol	-0.691	-0.398
AJ	0.442	-0.297
Bibs02	-0.273	-1.183
Bibs02c	-1.375	-0.467
BL6	1.107	1.501
BL6a	0.198	0.673
BXD01	1.094	0.48
BXD010	0.629	1.79
BXD011	0.448	1.392
BXD03	0.882	1.691
BXD04	1.131	1.224
BXD05	0.602	1.199
BXD06	0.535	1.382
BXD07	1.247	1.552
BXD08	0.253	1.23
BXD09	0.347	1.475
CAST	-1.23	-0.095
CCcont	0.917	1.406
DS01	-0.26	-0.197
DS02	-0.158	0.4
DS04	-0.453	0.873
DS0c	0.919	0.248
GP01	0.188	1.093
GP02	0.617	0.064
GP0c	0.61	1.136
NOD	-0.428	-0.864
NZO	-0.144	-0.445
PWK	0.067	-0.438
H37Rv_KO_CtpC	0.0	1.041
H37Rv_KO_CtpD	0.65	0.502
H37Rv_KO_Rv1272	0.227	2.178
H37Rv_KO_SugABC	0.348	1.968
H37Rv_KO_MbtN	1.484	0.827
Trans05	1.47	2.694
macrophage_unactivated	0.597	1.108
IL1	0.878	2.186
Rapamycin	0.973	0.976
Tcell	-1.007	0.635
GMCSF	0.89	1.217
IFNab	1.019	1.439
IFNg	0.505	0.938
IFNg_GMCSF1	0.0	0.317
Rv1432_day32	-0.055	0.0
Rv1565c_day32	0.231	0.951
secA2_input	-1.244	-1.442
delta_Rv3594	-0.122	-0.196
delta_Rv3717	-0.863	-0.751
delta_Rv3811	-0.379	-0.19
delta_Rv0954	-0.886	-0.678
PonA1	-0.792	-0.733
EccD1_KO	0.835	-1.223
EspI_KO	0.588	0.183
PE35_KO	0.601	1.015
PPE68_KO	1.171	1.277
glycerol2	0.238	-0.727
lignocerate	0.284	-0.632
oleate	1.259	-0.421
phosphatidylcholine	0.49	-0.597
acetate	-0.462	0.264
glucAc	-0.586	0.164
Rv0950ko	-0.172	0.694
Rv1096ko	0.477	1.475
Rv3684ko	0.675	-0.789
delta_otsA_trehalose	-0.075	-0.778