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 Rv1945/-:

update plot	correlation	link to info on gene
Rv1148c/-	(cc=0.6375)	info on Rv1148c/-
Rv2597/-	(cc=0.6085)	info on Rv2597/-
Rv1716/-	(cc=0.5593)	info on Rv1716/-
Rv3566c/nat	(cc=0.5159)	info on Rv3566c/nat
Rv1969/mce3D	(cc=0.5142)	info on Rv1969/mce3D
Rv1068c/PE_PGRS20	(cc=0.5015)	info on Rv1068c/PE_PGRS20
Rv2431c/PE25	(cc=0.4997)	info on Rv2431c/PE25
Rv3329/-	(cc=0.496)	info on Rv3329/-
Rv0961/-	(cc=0.4853)	info on Rv0961/-
Rv1101c/-	(cc=0.4654)	info on Rv1101c/-

Correlation of Rv1945/- with Rv2431c/PE25

Normalized LFCs for Rv1945/-:
(description and provenance of datasets)

	Rv1945/-	Rv2431c/PE25
Fe_supp_jason_reseq	-0.095	0.619
low_pH_jason_reseq	0.059	0.522
NO_jason_reseq	0.06	-0.914
B6_jason_reseq	-0.269	-0.36
MHCII_jason_reseq	-0.023	-0.217
Isoniazid02	-2.426	-0.931
Rifampicin4	0.168	-1.6
Ethambutol3	-2.053	-1.563
Meropenem3	-1.997	-1.653
Vancomycin16	-1.151	-0.921
Rv2680_day32	0.181	-0.087
H37Rv_KO_MarP	-0.109	-0.447
hypoxia_3wks	0.104	0.582
hypoxia_6wks	0.027	0.0
glycerol	-0.336	3.461
cholesterol	0.012	6.0
AJ	0.612	1.303
Bibs02	0.073	1.457
Bibs02c	0.717	1.199
BL6	-0.456	1.457
BL6a	0.446	2.072
BXD01	-0.536	0.827
BXD010	-0.674	0.551
BXD011	-0.571	2.085
BXD03	-0.374	1.534
BXD04	-0.524	1.689
BXD05	0.064	2.296
BXD06	-0.397	1.937
BXD07	-0.489	2.139
BXD08	-0.089	1.605
BXD09	-0.156	2.05
CAST	0.592	-0.192
CCcont	-0.888	1.232
DS01	0.578	3.744
DS02	0.95	3.294
DS04	1.382	3.536
DS0c	1.105	2.665
GP01	0.592	0.531
GP02	0.171	0.806
GP0c	-0.567	1.557
NOD	-0.229	1.523
NZO	0.707	0.962
PWK	0.31	2.947
H37Rv_KO_CtpC	0.065	1.81
H37Rv_KO_CtpD	1.035	1.079
H37Rv_KO_Rv1272	0.045	2.011
H37Rv_KO_SugABC	-0.233	1.484
H37Rv_KO_MbtN	0.388	0.09
Trans05	0.463	2.411
macrophage_unactivated	-0.849	0.211
IL1	0.35	0.561
Rapamycin	-0.77	0.233
Tcell	-0.587	0.72
GMCSF	-0.71	-0.304
IFNab	-0.813	0.668
IFNg	-0.342	0.786
IFNg_GMCSF1	-0.047	0.852
Rv1432_day32	-0.286	0.439
Rv1565c_day32	6.0	5.482
secA2_input	-0.338	-1.575
delta_Rv3594	-0.05	0.425
delta_Rv3717	0.573	0.174
delta_Rv3811	0.207	0.013
delta_Rv0954	0.572	1.122
PonA1	0.276	0.196
EccD1_KO	-0.368	-0.72
EspI_KO	1.141	-0.148
PE35_KO	0.303	0.639
PPE68_KO	1.011	0.64
glycerol2	-0.247	-0.013
lignocerate	-0.387	-0.468
oleate	0.333	0.801
phosphatidylcholine	0.122	0.162
acetate	-0.101	-0.753
glucAc	-0.701	-0.664
Rv0950ko	-0.317	0.084
Rv1096ko	-0.178	-1.197
Rv3684ko	0.495	-0.177
delta_otsA_trehalose	0.26	0.513