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 Rv2228c/-:

update plot	correlation	link to info on gene
Rv2973c/recG	(cc=0.4745)	info on Rv2973c/recG
Rv1067c/PE_PGRS19	(cc=0.474)	info on Rv1067c/PE_PGRS19
Rv2401/-	(cc=0.4534)	info on Rv2401/-
Rv2976c/ung	(cc=0.4413)	info on Rv2976c/ung
Rv2169c/-	(cc=0.4359)	info on Rv2169c/-
Rv0003/recF	(cc=0.4274)	info on Rv0003/recF
Rv3262/fbiB	(cc=0.425)	info on Rv3262/fbiB
Rv0778/cyp126	(cc=0.4213)	info on Rv0778/cyp126
Rv3674c/nth	(cc=0.4195)	info on Rv3674c/nth
Rv2922c/smc	(cc=0.4175)	info on Rv2922c/smc

Correlation of Rv2228c/- with Rv2169c/-

Normalized LFCs for Rv2228c/-:
(description and provenance of datasets)

	Rv2228c/-	Rv2169c/-
Fe_supp_jason_reseq	0.268	0.923
low_pH_jason_reseq	-1.134	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	1.206	0.0
MHCII_jason_reseq	0.315	0.135
Isoniazid02	-0.49	-0.796
Rifampicin4	-0.523	-2.134
Ethambutol3	-0.153	-0.958
Meropenem3	0.138	-1.109
Vancomycin16	-0.512	-2.457
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.065	-0.288
hypoxia_3wks	-0.427	-0.502
hypoxia_6wks	-0.223	-0.549
glycerol	2.07	0.0
cholesterol	0.159	0.0
AJ	0.0	0.0
Bibs02	-0.109	0.0
Bibs02c	-0.887	0.0
BL6	-0.074	0.0
BL6a	-0.377	0.0
BXD01	0.552	0.358
BXD010	0.206	0.0
BXD011	-0.335	0.0
BXD03	0.0	0.0
BXD04	0.932	0.0
BXD05	-0.256	0.0
BXD06	0.513	0.0
BXD07	0.0	0.138
BXD08	-0.35	0.0
BXD09	0.596	0.14
CAST	-0.284	0.0
CCcont	0.898	0.149
DS01	1.641	0.236
DS02	1.638	0.0
DS04	-0.115	0.0
DS0c	1.867	0.217
GP01	-0.607	0.0
GP02	-0.353	0.0
GP0c	-0.16	0.0
NOD	0.127	0.225
NZO	0.994	0.0
PWK	0.412	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	-0.084	0.0
H37Rv_KO_SugABC	-0.509	0.0
H37Rv_KO_MbtN	-0.061	0.0
Trans05	-0.444	0.0
macrophage_unactivated	0.83	0.0
IL1	-0.611	0.0
Rapamycin	-0.307	0.0
Tcell	0.59	0.45
GMCSF	0.478	0.0
IFNab	0.0	0.795
IFNg	-0.551	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-1.021	-1.832
delta_Rv3594	0.47	0.119
delta_Rv3717	-0.992	-1.067
delta_Rv3811	-1.172	-0.122
delta_Rv0954	-1.499	-1.096
PonA1	-0.286	0.0
EccD1_KO	0.178	0.454
EspI_KO	0.0	1.668
PE35_KO	-0.166	3.856
PPE68_KO	0.813	3.2
glycerol2	-1.202	-6.0
lignocerate	-1.55	-3.238
oleate	-0.345	-6.0
phosphatidylcholine	-0.803	-4.014
acetate	-0.663	-1.699
glucAc	-1.831	-2.833
Rv0950ko	0.172	-1.701
Rv1096ko	-0.555	-2.31
Rv3684ko	-0.393	-0.75
delta_otsA_trehalose	0.564	0.27