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 Rv2740/ephG:

update plot	correlation	link to info on gene
Rv3165c/-	(cc=0.4995)	info on Rv3165c/-
Rv2060/-	(cc=0.4512)	info on Rv2060/-
Rv2308/-	(cc=0.4399)	info on Rv2308/-
Rv1218c/-	(cc=0.4285)	info on Rv1218c/-
Rv2040c/-	(cc=0.4014)	info on Rv2040c/-
Rv1954A/-	(cc=0.3991)	info on Rv1954A/-
Rv1353c/-	(cc=0.3983)	info on Rv1353c/-
Rv2408/PE24	(cc=0.3907)	info on Rv2408/PE24
Rv1496/-	(cc=0.3907)	info on Rv1496/-
Rv2252/-	(cc=0.3881)	info on Rv2252/-

Correlation of Rv2740/ephG with Rv1496/-

Normalized LFCs for Rv2740/ephG:
(description and provenance of datasets)

	Rv2740/ephG	Rv1496/-
Fe_supp_jason_reseq	0.23	1.225
low_pH_jason_reseq	-0.579	-0.172
NO_jason_reseq	-0.735	-0.462
B6_jason_reseq	-0.318	-1.166
MHCII_jason_reseq	0.109	-1.939
Isoniazid02	-0.389	1.441
Rifampicin4	-0.127	-0.379
Ethambutol3	-0.264	1.459
Meropenem3	-0.299	0.184
Vancomycin16	-0.631	-0.289
Rv2680_day32	1.128	0.208
H37Rv_KO_MarP	-0.292	-0.47
hypoxia_3wks	-0.67	0.67
hypoxia_6wks	-0.238	-0.299
glycerol	-0.307	0.186
cholesterol	-0.285	0.81
AJ	-0.183	-1.002
Bibs02	-0.585	-0.152
Bibs02c	-0.77	-1.061
BL6	-0.372	0.926
BL6a	0.281	-0.271
BXD01	-0.235	0.692
BXD010	0.365	1.726
BXD011	0.709	0.963
BXD03	0.492	0.867
BXD04	-0.043	2.068
BXD05	0.429	0.953
BXD06	0.072	0.514
BXD07	0.409	0.875
BXD08	0.616	1.377
BXD09	0.427	0.786
CAST	0.327	-0.584
CCcont	-0.113	1.924
DS01	-1.258	-1.138
DS02	-1.3	-2.568
DS04	0.066	-1.436
DS0c	-0.757	-1.403
GP01	0.403	2.198
GP02	0.014	0.113
GP0c	0.834	1.915
NOD	-0.135	-1.453
NZO	0.428	-1.118
PWK	-0.675	0.122
H37Rv_KO_CtpC	-0.598	-0.379
H37Rv_KO_CtpD	0.479	1.685
H37Rv_KO_Rv1272	0.103	0.324
H37Rv_KO_SugABC	-2.096	-0.641
H37Rv_KO_MbtN	-0.306	1.89
Trans05	0.053	0.882
macrophage_unactivated	-0.227	0.319
IL1	0.448	0.825
Rapamycin	0.672	1.126
Tcell	-0.635	0.31
GMCSF	0.734	1.516
IFNab	0.36	0.538
IFNg	0.222	1.761
IFNg_GMCSF1	-0.544	0.789
Rv1432_day32	-0.327	0.0
Rv1565c_day32	0.826	0.058
secA2_input	-2.057	-0.873
delta_Rv3594	0.217	-0.699
delta_Rv3717	1.121	-0.162
delta_Rv3811	-0.311	0.251
delta_Rv0954	-1.55	-1.087
PonA1	0.187	0.316
EccD1_KO	1.217	1.059
EspI_KO	0.704	-0.513
PE35_KO	0.933	0.318
PPE68_KO	1.094	0.512
glycerol2	0.404	-0.509
lignocerate	0.479	-0.061
oleate	-0.713	0.323
phosphatidylcholine	0.625	0.141
acetate	0.356	-0.042
glucAc	0.869	-0.318
Rv0950ko	0.241	1.173
Rv1096ko	0.47	0.875
Rv3684ko	-0.174	1.13
delta_otsA_trehalose	0.404	0.014