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 Rv1696/recN:

update plot	correlation	link to info on gene
Rv2392/cysH	(cc=0.4219)	info on Rv2392/cysH
Rv2521/bcp	(cc=0.3942)	info on Rv2521/bcp
Rv1714/-	(cc=0.3923)	info on Rv1714/-
Rv3550/echA20	(cc=0.3823)	info on Rv3550/echA20
Rv1406/fmt	(cc=0.3797)	info on Rv1406/fmt
Rv2530A/vapB39	(cc=0.3746)	info on Rv2530A/vapB39
Rv1188/-	(cc=0.3721)	info on Rv1188/-
Rv0633c/-	(cc=0.3673)	info on Rv0633c/-
Rv0650/-	(cc=0.3607)	info on Rv0650/-
Rv1534/-	(cc=0.3585)	info on Rv1534/-

Correlation of Rv1696/recN with Rv0650/-

Normalized LFCs for Rv1696/recN:
(description and provenance of datasets)

	Rv1696/recN	Rv0650/-
Fe_supp_jason_reseq	-0.218	-1.301
low_pH_jason_reseq	1.051	-0.748
NO_jason_reseq	1.299	-0.772
B6_jason_reseq	-1.184	-0.437
MHCII_jason_reseq	-0.494	0.252
Isoniazid02	0.265	0.639
Rifampicin4	-0.076	1.481
Ethambutol3	-0.14	1.792
Meropenem3	-0.103	0.304
Vancomycin16	0.0	0.735
Rv2680_day32	0.816	0.326
H37Rv_KO_MarP	-0.512	0.446
hypoxia_3wks	0.171	-0.235
hypoxia_6wks	-0.495	-1.503
glycerol	0.635	2.342
cholesterol	0.329	1.387
AJ	0.729	1.168
Bibs02	-1.274	0.503
Bibs02c	-1.458	1.44
BL6	-0.189	0.63
BL6a	-0.577	0.684
BXD01	0.036	-0.164
BXD010	-0.194	0.486
BXD011	0.07	-0.383
BXD03	-0.446	-0.73
BXD04	0.1	-0.692
BXD05	0.212	-1.163
BXD06	-0.492	-0.37
BXD07	0.283	-0.042
BXD08	0.499	0.366
BXD09	0.186	-0.235
CAST	-0.275	0.402
CCcont	0.531	0.913
DS01	0.792	1.738
DS02	0.06	1.47
DS04	-0.715	-0.422
DS0c	0.979	1.466
GP01	0.808	0.919
GP02	-0.074	0.057
GP0c	0.204	0.669
NOD	-0.34	0.805
NZO	0.162	0.308
PWK	-0.114	0.627
H37Rv_KO_CtpC	-1.32	-0.752
H37Rv_KO_CtpD	0.596	0.661
H37Rv_KO_Rv1272	0.761	-0.095
H37Rv_KO_SugABC	0.63	0.316
H37Rv_KO_MbtN	-1.047	-2.29
Trans05	0.267	0.298
macrophage_unactivated	-1.016	0.574
IL1	0.463	2.058
Rapamycin	0.479	0.672
Tcell	-0.137	-0.368
GMCSF	0.412	0.322
IFNab	0.124	0.846
IFNg	0.0	0.668
IFNg_GMCSF1	-0.698	0.927
Rv1432_day32	-1.027	0.692
Rv1565c_day32	1.308	-0.415
secA2_input	0.631	1.669
delta_Rv3594	0.985	-0.463
delta_Rv3717	0.774	0.515
delta_Rv3811	0.129	-0.076
delta_Rv0954	0.416	1.26
PonA1	0.84	0.375
EccD1_KO	0.102	1.151
EspI_KO	-0.473	0.325
PE35_KO	-0.093	-0.814
PPE68_KO	0.195	-0.566
glycerol2	-0.601	0.137
lignocerate	0.278	0.788
oleate	-0.457	-0.544
phosphatidylcholine	-0.181	0.416
acetate	1.041	-0.115
glucAc	0.804	0.453
Rv0950ko	0.446	1.493
Rv1096ko	2.247	3.088
Rv3684ko	1.608	3.76
delta_otsA_trehalose	-1.369	-0.197