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 Rv2262c/-:

update plot	correlation	link to info on gene
Rv0940c/-	(cc=0.4887)	info on Rv0940c/-
Rv1664/pks9	(cc=0.4783)	info on Rv1664/pks9
Rv0397A/-	(cc=0.4751)	info on Rv0397A/-
Rv1947/-	(cc=0.4718)	info on Rv1947/-
Rv1726/-	(cc=0.469)	info on Rv1726/-
Rv3664c/dppC	(cc=0.4551)	info on Rv3664c/dppC
Rv3150/nuoF	(cc=0.4482)	info on Rv3150/nuoF
Rv3397c/phyA	(cc=0.4447)	info on Rv3397c/phyA
Rv3116/moeB2	(cc=0.44)	info on Rv3116/moeB2
Rv2345/-	(cc=0.4363)	info on Rv2345/-

Correlation of Rv2262c/- with Rv1664/pks9

Normalized LFCs for Rv2262c/-:
(description and provenance of datasets)

	Rv2262c/-	Rv1664/pks9
Fe_supp_jason_reseq	-0.979	0.611
low_pH_jason_reseq	0.082	0.045
NO_jason_reseq	0.252	0.142
B6_jason_reseq	-0.033	-0.828
MHCII_jason_reseq	-0.1	-0.823
Isoniazid02	-1.061	-0.615
Rifampicin4	0.915	0.317
Ethambutol3	-0.904	-0.916
Meropenem3	-1.549	-0.43
Vancomycin16	-0.517	-0.066
Rv2680_day32	-0.793	-0.348
H37Rv_KO_MarP	0.172	0.185
hypoxia_3wks	0.439	0.1
hypoxia_6wks	-0.146	-0.109
glycerol	0.328	0.835
cholesterol	-0.804	0.203
AJ	0.061	-0.294
Bibs02	-0.221	-0.642
Bibs02c	-1.356	-0.735
BL6	1.454	0.357
BL6a	-0.089	0.426
BXD01	0.885	0.843
BXD010	0.554	0.699
BXD011	0.066	0.761
BXD03	-0.098	0.258
BXD04	0.461	0.914
BXD05	0.209	1.375
BXD06	0.323	0.775
BXD07	0.591	0.961
BXD08	0.598	0.75
BXD09	0.207	0.524
CAST	0.374	-0.215
CCcont	0.574	0.618
DS01	0.14	0.33
DS02	0.978	0.246
DS04	0.85	0.597
DS0c	0.555	0.717
GP01	-0.211	1.902
GP02	-0.539	-0.078
GP0c	-0.41	0.564
NOD	-0.735	-0.21
NZO	-0.605	-0.061
PWK	-0.296	-0.315
H37Rv_KO_CtpC	0.684	0.828
H37Rv_KO_CtpD	-0.298	1.22
H37Rv_KO_Rv1272	0.552	1.456
H37Rv_KO_SugABC	-0.301	1.39
H37Rv_KO_MbtN	0.611	0.294
Trans05	0.788	1.335
macrophage_unactivated	0.193	0.997
IL1	0.062	0.866
Rapamycin	0.31	1.182
Tcell	0.694	1.105
GMCSF	0.108	1.017
IFNab	0.124	0.955
IFNg	-0.35	0.906
IFNg_GMCSF1	0.031	0.525
Rv1432_day32	-0.147	-0.142
Rv1565c_day32	0.466	0.531
secA2_input	-0.631	-0.65
delta_Rv3594	-0.281	-0.311
delta_Rv3717	-0.257	-1.008
delta_Rv3811	0.37	-0.47
delta_Rv0954	-0.048	-0.74
PonA1	-0.756	-0.744
EccD1_KO	-0.187	-0.549
EspI_KO	0.451	-0.935
PE35_KO	-0.055	-0.563
PPE68_KO	-0.598	-0.454
glycerol2	0.165	-0.862
lignocerate	-0.212	-0.721
oleate	0.242	-0.364
phosphatidylcholine	0.261	-0.623
acetate	-0.332	-0.806
glucAc	-0.638	-0.808
Rv0950ko	-0.317	-0.371
Rv1096ko	0.422	0.277
Rv3684ko	-0.383	-0.665
delta_otsA_trehalose	1.545	1.396