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 Rv3235/-:

update plot	correlation	link to info on gene
Rv0630c/recB	(cc=0.4396)	info on Rv0630c/recB
Rv0960/vapC9	(cc=0.427)	info on Rv0960/vapC9
Rv2066/cobI	(cc=0.3785)	info on Rv2066/cobI
Rv1001/arcA	(cc=0.3773)	info on Rv1001/arcA
Rv1759c/wag22	(cc=0.3737)	info on Rv1759c/wag22
Rv3026c/-	(cc=0.3731)	info on Rv3026c/-
Rv3084/lipR	(cc=0.3616)	info on Rv3084/lipR
Rv0631c/recC	(cc=0.3559)	info on Rv0631c/recC
Rv0613c/-	(cc=0.3504)	info on Rv0613c/-
Rv1867/-	(cc=0.3475)	info on Rv1867/-

Correlation of Rv3235/- with Rv1867/-

Normalized LFCs for Rv3235/-:
(description and provenance of datasets)

	Rv3235/-	Rv1867/-
Fe_supp_jason_reseq	-2.433	-0.523
low_pH_jason_reseq	-1.323	-0.887
NO_jason_reseq	-1.25	-0.21
B6_jason_reseq	-1.305	-0.428
MHCII_jason_reseq	-0.674	-0.143
Isoniazid02	-0.317	-0.773
Rifampicin4	0.994	0.42
Ethambutol3	-0.101	-0.623
Meropenem3	-0.066	-0.601
Vancomycin16	0.034	-0.483
Rv2680_day32	1.05	0.794
H37Rv_KO_MarP	0.586	0.442
hypoxia_3wks	-1.531	-0.415
hypoxia_6wks	-0.509	0.553
glycerol	0.629	-0.625
cholesterol	0.44	0.101
AJ	-0.748	0.378
Bibs02	0.735	0.529
Bibs02c	-0.068	-0.261
BL6	-1.734	0.439
BL6a	0.201	0.113
BXD01	-0.162	0.017
BXD010	-1.012	0.23
BXD011	-1.873	0.149
BXD03	0.935	-0.693
BXD04	-1.191	-0.191
BXD05	-0.918	0.61
BXD06	-1.285	0.109
BXD07	-0.406	0.507
BXD08	-1.556	-0.71
BXD09	-1.018	-0.009
CAST	-0.232	-0.445
CCcont	-0.64	0.26
DS01	0.601	-0.079
DS02	1.027	-0.117
DS04	0.916	0.098
DS0c	-1.039	-0.729
GP01	-0.054	0.596
GP02	0.464	0.931
GP0c	0.907	0.69
NOD	0.0	-0.199
NZO	-1.058	-0.37
PWK	0.611	-0.119
H37Rv_KO_CtpC	0.034	-0.109
H37Rv_KO_CtpD	0.177	0.951
H37Rv_KO_Rv1272	-0.336	0.23
H37Rv_KO_SugABC	0.54	0.733
H37Rv_KO_MbtN	0.414	0.677
Trans05	-1.866	0.161
macrophage_unactivated	-0.189	-0.259
IL1	4.9	0.914
Rapamycin	-0.577	0.285
Tcell	0.0	-0.267
GMCSF	1.077	0.457
IFNab	-0.886	0.647
IFNg	-2.443	0.556
IFNg_GMCSF1	1.486	0.075
Rv1432_day32	0.0	0.394
Rv1565c_day32	0.55	0.137
secA2_input	-1.882	-1.119
delta_Rv3594	0.06	-0.015
delta_Rv3717	0.31	-0.062
delta_Rv3811	-0.819	0.085
delta_Rv0954	0.947	0.025
PonA1	-0.813	-0.012
EccD1_KO	-0.289	0.612
EspI_KO	0.322	0.354
PE35_KO	0.636	0.169
PPE68_KO	0.726	0.278
glycerol2	-0.796	0.064
lignocerate	-0.24	0.811
oleate	-0.481	-0.71
phosphatidylcholine	-0.445	0.343
acetate	0.82	0.938
glucAc	0.298	0.88
Rv0950ko	0.633	0.401
Rv1096ko	0.787	0.0
Rv3684ko	0.341	0.802
delta_otsA_trehalose	-0.939	0.242