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 Rv1112/-:

update plot	correlation	link to info on gene
Rv3269/-	(cc=0.6543)	info on Rv3269/-
Rv1008/tatD	(cc=0.6147)	info on Rv1008/tatD
Rv1170/mshB	(cc=0.6083)	info on Rv1170/mshB
Rv3624c/hpt	(cc=0.5741)	info on Rv3624c/hpt
Rv3755c/-	(cc=0.5657)	info on Rv3755c/-
Rv0819/mshD	(cc=0.558)	info on Rv0819/mshD
Rv2131c/cysQ	(cc=0.5561)	info on Rv2131c/cysQ
Rv2404c/lepA	(cc=0.5434)	info on Rv2404c/lepA
Rv1908c/katG	(cc=0.5319)	info on Rv1908c/katG
Rv3715c/recR	(cc=0.53)	info on Rv3715c/recR

Correlation of Rv1112/- with Rv1170/mshB

Normalized LFCs for Rv1112/-:
(description and provenance of datasets)

	Rv1112/-	Rv1170/mshB
Fe_supp_jason_reseq	1.901	3.375
low_pH_jason_reseq	-1.571	0.634
NO_jason_reseq	0.315	1.273
B6_jason_reseq	-0.913	0.538
MHCII_jason_reseq	0.0	0.0
Isoniazid02	3.87	5.619
Rifampicin4	0.712	2.404
Ethambutol3	1.414	2.042
Meropenem3	0.426	-0.315
Vancomycin16	1.602	1.955
Rv2680_day32	0.109	0.0
H37Rv_KO_MarP	2.428	1.693
hypoxia_3wks	-2.68	-3.026
hypoxia_6wks	-2.533	-1.361
glycerol	2.487	1.355
cholesterol	1.62	2.856
AJ	1.78	1.287
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	1.574	0.0
BL6a	1.964	0.377
BXD01	1.496	1.301
BXD010	1.739	0.787
BXD011	0.612	0.243
BXD03	1.146	0.573
BXD04	1.588	1.184
BXD05	1.241	0.473
BXD06	2.098	1.333
BXD07	0.809	0.264
BXD08	1.227	1.096
BXD09	2.005	1.346
CAST	1.458	0.23
CCcont	4.277	2.716
DS01	0.551	0.0
DS02	0.35	0.0
DS04	1.32	0.37
DS0c	0.652	0.0
GP01	0.36	0.099
GP02	-0.159	0.0
GP0c	-0.248	0.248
NOD	2.071	0.789
NZO	1.357	1.107
PWK	0.715	0.539
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	1.689	1.159
H37Rv_KO_Rv1272	0.753	0.0
H37Rv_KO_SugABC	1.666	0.099
H37Rv_KO_MbtN	1.959	0.0
Trans05	0.628	0.249
macrophage_unactivated	0.571	0.0
IL1	-1.326	0.0
Rapamycin	-0.307	0.0
Tcell	0.303	0.0
GMCSF	-0.85	0.0
IFNab	0.795	0.0
IFNg	-1.563	0.0
IFNg_GMCSF1	-0.647	0.0
Rv1432_day32	1.155	0.0
Rv1565c_day32	-0.256	0.415
secA2_input	-0.676	-1.791
delta_Rv3594	4.577	0.125
delta_Rv3717	4.406	-0.736
delta_Rv3811	3.248	0.162
delta_Rv0954	0.969	1.594
PonA1	-0.245	0.325
EccD1_KO	-1.542	-4.812
EspI_KO	-1.879	-3.933
PE35_KO	-0.548	0.72
PPE68_KO	-0.902	-1.145
glycerol2	0.395	-0.298
lignocerate	-0.764	-1.734
oleate	-0.588	-1.629
phosphatidylcholine	-1.751	-2.473
acetate	1.536	0.136
glucAc	2.08	0.242
Rv0950ko	0.862	0.118
Rv1096ko	0.398	0.962
Rv3684ko	0.829	2.423
delta_otsA_trehalose	0.4	-1.375