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 Rv3070/-:

update plot	correlation	link to info on gene
Rv1662/pks8	(cc=0.5061)	info on Rv1662/pks8
Rv1419/-	(cc=0.4987)	info on Rv1419/-
Rv0276/-	(cc=0.4657)	info on Rv0276/-
Rv2495c/bkdC	(cc=0.4624)	info on Rv2495c/bkdC
Rv0827c/kmtR	(cc=0.4484)	info on Rv0827c/kmtR
Rv3140/fadE23	(cc=0.4449)	info on Rv3140/fadE23
Rv2211c/gcvT	(cc=0.4339)	info on Rv2211c/gcvT
Rv3626c/-	(cc=0.4311)	info on Rv3626c/-
Rv2833c/ugpB	(cc=0.4288)	info on Rv2833c/ugpB
Rv2767c/-	(cc=0.4193)	info on Rv2767c/-

Correlation of Rv3070/- with Rv2767c/-

Normalized LFCs for Rv3070/-:
(description and provenance of datasets)

	Rv3070/-	Rv2767c/-
Fe_supp_jason_reseq	-0.529	0.453
low_pH_jason_reseq	-0.878	-0.731
NO_jason_reseq	-0.494	-0.302
B6_jason_reseq	-1.15	-0.164
MHCII_jason_reseq	-0.669	0.028
Isoniazid02	-0.035	-0.573
Rifampicin4	-0.996	-1.384
Ethambutol3	-0.524	-1.338
Meropenem3	-0.422	-1.438
Vancomycin16	-0.369	-1.228
Rv2680_day32	0.899	1.591
H37Rv_KO_MarP	0.233	0.683
hypoxia_3wks	-0.088	-0.136
hypoxia_6wks	0.28	-0.89
glycerol	-0.788	-0.769
cholesterol	-0.981	-0.311
AJ	1.077	0.072
Bibs02	0.838	-0.23
Bibs02c	1.085	1.449
BL6	0.327	0.825
BL6a	1.378	1.465
BXD01	0.993	-0.782
BXD010	0.792	0.862
BXD011	0.285	0.391
BXD03	1.018	0.458
BXD04	0.43	0.09
BXD05	0.237	0.533
BXD06	1.196	0.238
BXD07	0.75	0.601
BXD08	0.944	0.009
BXD09	0.991	0.391
CAST	0.586	-0.195
CCcont	1.06	0.018
DS01	-0.068	0.332
DS02	0.469	0.488
DS04	1.018	-0.062
DS0c	0.273	0.888
GP01	-0.706	0.77
GP02	-1.474	0.271
GP0c	-0.117	-0.427
NOD	1.015	0.215
NZO	-0.724	0.428
PWK	0.735	0.084
H37Rv_KO_CtpC	0.934	0.685
H37Rv_KO_CtpD	0.44	0.523
H37Rv_KO_Rv1272	0.637	0.534
H37Rv_KO_SugABC	-1.705	-1.813
H37Rv_KO_MbtN	-1.164	-0.631
Trans05	0.445	0.484
macrophage_unactivated	0.726	-0.455
IL1	0.771	0.543
Rapamycin	0.393	0.654
Tcell	0.626	0.218
GMCSF	0.317	0.85
IFNab	0.212	0.381
IFNg	0.831	0.898
IFNg_GMCSF1	1.241	0.361
Rv1432_day32	-0.257	0.51
Rv1565c_day32	0.12	0.24
secA2_input	-0.177	-0.302
delta_Rv3594	1.054	-0.277
delta_Rv3717	-1.258	-0.327
delta_Rv3811	0.043	-0.694
delta_Rv0954	0.89	0.58
PonA1	0.177	0.185
EccD1_KO	-0.082	1.223
EspI_KO	-0.736	1.417
PE35_KO	1.138	0.411
PPE68_KO	0.08	0.125
glycerol2	0.342	-0.835
lignocerate	0.485	-0.432
oleate	0.116	-0.543
phosphatidylcholine	0.312	-0.618
acetate	0.146	-0.308
glucAc	0.102	-0.141
Rv0950ko	0.709	-0.265
Rv1096ko	1.173	0.229
Rv3684ko	2.227	0.531
delta_otsA_trehalose	0.049	-0.204