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 Rv3817/-:

update plot	correlation	link to info on gene
Rv3509c/ilvX	(cc=0.4806)	info on Rv3509c/ilvX
Rv1506c/-	(cc=0.4616)	info on Rv1506c/-
Rv1313c/-	(cc=0.4565)	info on Rv1313c/-
Rv3098c/-	(cc=0.4456)	info on Rv3098c/-
Rv0540/-	(cc=0.4424)	info on Rv0540/-
Rv0755c/PPE12	(cc=0.4418)	info on Rv0755c/PPE12
Rv2303c/-	(cc=0.4276)	info on Rv2303c/-
Rv3183/-	(cc=0.4269)	info on Rv3183/-
Rv0546c/-	(cc=0.4196)	info on Rv0546c/-
Rv0835/lpqQ	(cc=0.4142)	info on Rv0835/lpqQ

Correlation of Rv3817/- with Rv3509c/ilvX

Normalized LFCs for Rv3817/-:
(description and provenance of datasets)

	Rv3817/-	Rv3509c/ilvX
Fe_supp_jason_reseq	1.26	-0.081
low_pH_jason_reseq	-0.504	-0.375
NO_jason_reseq	-0.725	-0.257
B6_jason_reseq	-0.757	0.367
MHCII_jason_reseq	1.194	0.362
Isoniazid02	0.215	1.147
Rifampicin4	0.588	0.55
Ethambutol3	0.107	0.899
Meropenem3	0.883	0.328
Vancomycin16	0.605	0.727
Rv2680_day32	-1.131	-0.207
H37Rv_KO_MarP	-0.063	0.302
hypoxia_3wks	0.0	-0.104
hypoxia_6wks	-0.493	-0.355
glycerol	0.499	0.699
cholesterol	-0.435	0.869
AJ	0.758	0.282
Bibs02	1.646	0.34
Bibs02c	1.46	0.45
BL6	1.451	0.502
BL6a	1.4	0.458
BXD01	0.442	0.516
BXD010	0.168	0.03
BXD011	2.88	0.68
BXD03	-1.417	0.047
BXD04	-0.59	0.408
BXD05	0.422	-0.064
BXD06	0.068	0.39
BXD07	-0.739	0.174
BXD08	-0.496	-0.011
BXD09	-0.297	0.126
CAST	-0.344	0.207
CCcont	-1.082	-0.281
DS01	0.518	0.409
DS02	-1.038	0.28
DS04	-0.453	0.835
DS0c	-1.158	0.594
GP01	0.257	-0.119
GP02	-0.397	-0.02
GP0c	-1.245	-0.314
NOD	1.222	0.714
NZO	-0.6	-0.048
PWK	1.128	0.415
H37Rv_KO_CtpC	0.85	-0.006
H37Rv_KO_CtpD	0.703	0.044
H37Rv_KO_Rv1272	0.095	0.167
H37Rv_KO_SugABC	1.102	0.471
H37Rv_KO_MbtN	1.999	0.257
Trans05	1.887	0.094
macrophage_unactivated	-2.219	-0.732
IL1	-0.267	-0.602
Rapamycin	-1.436	-0.868
Tcell	0.222	-0.459
GMCSF	-2.419	-0.428
IFNab	-1.874	-0.856
IFNg	-0.943	-0.877
IFNg_GMCSF1	-2.297	0.226
Rv1432_day32	0.0	0.756
Rv1565c_day32	-0.706	0.175
secA2_input	0.097	-0.189
delta_Rv3594	0.173	0.783
delta_Rv3717	0.036	0.039
delta_Rv3811	1.735	0.651
delta_Rv0954	-0.379	0.915
PonA1	0.731	0.743
EccD1_KO	0.664	0.072
EspI_KO	1.235	-0.125
PE35_KO	0.895	-0.064
PPE68_KO	0.595	-0.384
glycerol2	-0.437	-0.174
lignocerate	-1.268	-0.358
oleate	-0.179	-0.33
phosphatidylcholine	-0.115	-0.209
acetate	-1.945	-0.849
glucAc	-2.552	-0.171
Rv0950ko	0.992	0.612
Rv1096ko	0.742	0.953
Rv3684ko	-0.838	0.4
delta_otsA_trehalose	0.0	-0.209