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 Rv1422/-:

update plot	correlation	link to info on gene
Rv3919c/gid	(cc=0.5365)	info on Rv3919c/gid
Rv1079/metB	(cc=0.5169)	info on Rv1079/metB
Rv2978c/-	(cc=0.5113)	info on Rv2978c/-
Rv1633/uvrB	(cc=0.4985)	info on Rv1633/uvrB
Rv3841/bfrB	(cc=0.498)	info on Rv3841/bfrB
Rv2366c/-	(cc=0.4953)	info on Rv2366c/-
Rv0653c/-	(cc=0.4941)	info on Rv0653c/-
Rv2734/-	(cc=0.4927)	info on Rv2734/-
Rv0150c/-	(cc=0.4792)	info on Rv0150c/-
Rv0956/purN	(cc=0.4749)	info on Rv0956/purN

Correlation of Rv1422/- with Rv2978c/-

Normalized LFCs for Rv1422/-:
(description and provenance of datasets)

	Rv1422/-	Rv2978c/-
Fe_supp_jason_reseq	1.358	-0.052
low_pH_jason_reseq	-0.234	-0.261
NO_jason_reseq	0.068	-0.221
B6_jason_reseq	-1.947	-1.303
MHCII_jason_reseq	-1.4	-1.184
Isoniazid02	-0.579	0.611
Rifampicin4	0.138	0.753
Ethambutol3	0.753	1.126
Meropenem3	-0.383	0.223
Vancomycin16	-1.61	-0.146
Rv2680_day32	-0.19	-0.586
H37Rv_KO_MarP	2.572	0.179
hypoxia_3wks	-2.237	0.211
hypoxia_6wks	-1.8	0.762
glycerol	-2.06	0.0
cholesterol	-0.114	0.526
AJ	-1.262	0.605
Bibs02	-1.191	-0.49
Bibs02c	-0.233	0.377
BL6	1.148	0.505
BL6a	0.199	0.517
BXD01	0.852	0.473
BXD010	1.191	0.334
BXD011	-0.186	0.445
BXD03	0.191	1.353
BXD04	0.518	0.341
BXD05	1.044	-0.054
BXD06	1.083	0.263
BXD07	0.961	1.436
BXD08	0.636	0.367
BXD09	0.617	0.491
CAST	-0.546	0.377
CCcont	0.531	0.478
DS01	0.0	0.387
DS02	-1.676	-0.944
DS04	-1.32	-1.154
DS0c	-1.413	-0.696
GP01	1.051	0.257
GP02	0.406	0.627
GP0c	1.159	0.169
NOD	-1.956	0.0
NZO	-0.757	-0.806
PWK	-0.465	0.418
H37Rv_KO_CtpC	0.525	0.32
H37Rv_KO_CtpD	0.276	0.786
H37Rv_KO_Rv1272	0.218	-0.086
H37Rv_KO_SugABC	-0.293	1.188
H37Rv_KO_MbtN	0.959	-0.809
Trans05	-0.386	0.38
macrophage_unactivated	-0.578	0.922
IL1	-1.163	0.234
Rapamycin	-0.632	-0.7
Tcell	-0.485	-0.619
GMCSF	0.356	0.0
IFNab	-0.03	-0.2
IFNg	-0.428	-0.609
IFNg_GMCSF1	-0.097	0.342
Rv1432_day32	-0.039	0.541
Rv1565c_day32	-2.854	-3.101
secA2_input	-0.762	0.095
delta_Rv3594	2.034	1.892
delta_Rv3717	1.443	0.165
delta_Rv3811	1.377	0.617
delta_Rv0954	1.081	1.336
PonA1	-1.154	1.051
EccD1_KO	2.625	2.601
EspI_KO	0.918	2.524
PE35_KO	1.488	2.018
PPE68_KO	1.561	2.323
glycerol2	0.191	-0.112
lignocerate	-3.01	-0.51
oleate	-1.591	0.159
phosphatidylcholine	-3.013	0.0
acetate	0.043	-1.358
glucAc	-0.38	-1.16
Rv0950ko	0.488	0.0
Rv1096ko	-0.217	0.76
Rv3684ko	0.033	0.219
delta_otsA_trehalose	1.62	-0.659