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 Rv2308/-

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

	Rv2740/ephG	Rv2308/-
Fe_supp_jason_reseq	0.23	0.702
low_pH_jason_reseq	-0.579	-0.744
NO_jason_reseq	-0.735	-0.407
B6_jason_reseq	-0.318	0.621
MHCII_jason_reseq	0.109	-0.272
Isoniazid02	-0.389	-0.925
Rifampicin4	-0.127	0.412
Ethambutol3	-0.264	-0.624
Meropenem3	-0.299	-0.353
Vancomycin16	-0.631	-0.332
Rv2680_day32	1.128	0.79
H37Rv_KO_MarP	-0.292	-0.035
hypoxia_3wks	-0.67	-0.144
hypoxia_6wks	-0.238	-0.823
glycerol	-0.307	-1.22
cholesterol	-0.285	-0.363
AJ	-0.183	0.02
Bibs02	-0.585	-0.025
Bibs02c	-0.77	0.009
BL6	-0.372	0.099
BL6a	0.281	0.165
BXD01	-0.235	-1.147
BXD010	0.365	0.296
BXD011	0.709	-0.042
BXD03	0.492	-0.277
BXD04	-0.043	-0.017
BXD05	0.429	0.355
BXD06	0.072	-0.209
BXD07	0.409	-0.269
BXD08	0.616	-0.237
BXD09	0.427	0.099
CAST	0.327	-0.075
CCcont	-0.113	0.233
DS01	-1.258	-0.212
DS02	-1.3	-0.009
DS04	0.066	-0.263
DS0c	-0.757	-0.328
GP01	0.403	-0.421
GP02	0.014	-0.444
GP0c	0.834	-0.318
NOD	-0.135	-0.304
NZO	0.428	0.319
PWK	-0.675	0.467
H37Rv_KO_CtpC	-0.598	-0.171
H37Rv_KO_CtpD	0.479	0.891
H37Rv_KO_Rv1272	0.103	-0.033
H37Rv_KO_SugABC	-2.096	-0.559
H37Rv_KO_MbtN	-0.306	0.555
Trans05	0.053	0.596
macrophage_unactivated	-0.227	0.672
IL1	0.448	0.131
Rapamycin	0.672	0.233
Tcell	-0.635	-0.518
GMCSF	0.734	0.298
IFNab	0.36	0.526
IFNg	0.222	0.516
IFNg_GMCSF1	-0.544	0.437
Rv1432_day32	-0.327	0.016
Rv1565c_day32	0.826	-0.471
secA2_input	-2.057	-0.941
delta_Rv3594	0.217	-0.093
delta_Rv3717	1.121	0.096
delta_Rv3811	-0.311	0.291
delta_Rv0954	-1.55	-0.665
PonA1	0.187	0.338
EccD1_KO	1.217	0.069
EspI_KO	0.704	0.165
PE35_KO	0.933	0.403
PPE68_KO	1.094	0.186
glycerol2	0.404	0.989
lignocerate	0.479	1.419
oleate	-0.713	-0.166
phosphatidylcholine	0.625	0.989
acetate	0.356	0.786
glucAc	0.869	1.334
Rv0950ko	0.241	0.241
Rv1096ko	0.47	-0.51
Rv3684ko	-0.174	0.0
delta_otsA_trehalose	0.404	0.958