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 Rv0461/-:

update plot	correlation	link to info on gene
Rv3448/eccD4	(cc=0.5455)	info on Rv3448/eccD4
Rv1429/-	(cc=0.5174)	info on Rv1429/-
Rv0419/lpqM	(cc=0.5032)	info on Rv0419/lpqM
Rv1287/-	(cc=0.4909)	info on Rv1287/-
Rv2613c/-	(cc=0.4454)	info on Rv2613c/-
Rv3058c/-	(cc=0.442)	info on Rv3058c/-
Rv3060c/-	(cc=0.4415)	info on Rv3060c/-
Rv1291c/-	(cc=0.433)	info on Rv1291c/-
Rv1171/-	(cc=0.4315)	info on Rv1171/-
Rv0837c/-	(cc=0.4289)	info on Rv0837c/-

Correlation of Rv0461/- with Rv0419/lpqM

Normalized LFCs for Rv0461/-:
(description and provenance of datasets)

	Rv0461/-	Rv0419/lpqM
Fe_supp_jason_reseq	0.341	0.534
low_pH_jason_reseq	0.027	-0.35
NO_jason_reseq	0.15	-0.659
B6_jason_reseq	0.173	0.22
MHCII_jason_reseq	0.809	0.753
Isoniazid02	-0.893	-0.453
Rifampicin4	0.942	0.68
Ethambutol3	0.61	-0.197
Meropenem3	-0.132	-0.627
Vancomycin16	-0.817	0.17
Rv2680_day32	0.367	0.717
H37Rv_KO_MarP	1.28	0.234
hypoxia_3wks	-0.096	-0.582
hypoxia_6wks	-0.328	-0.267
glycerol	0.255	-0.906
cholesterol	0.336	-0.252
AJ	0.077	0.328
Bibs02	-0.519	-0.416
Bibs02c	0.047	0.383
BL6	-0.569	0.157
BL6a	0.07	-0.118
BXD01	-0.041	-0.558
BXD010	-0.247	-0.196
BXD011	-0.224	-0.415
BXD03	-0.152	-0.1
BXD04	0.138	-0.572
BXD05	-0.264	-0.524
BXD06	-0.579	-0.528
BXD07	-0.047	-0.05
BXD08	0.559	-0.31
BXD09	-0.175	-0.07
CAST	-0.309	-0.282
CCcont	-0.248	-0.291
DS01	-0.214	-0.349
DS02	-0.03	0.019
DS04	0.306	0.197
DS0c	-0.093	0.365
GP01	-0.795	-0.022
GP02	0.389	-0.396
GP0c	-0.365	-1.134
NOD	-0.05	0.255
NZO	-0.056	-0.118
PWK	-0.438	0.293
H37Rv_KO_CtpC	0.248	-0.685
H37Rv_KO_CtpD	-0.111	-0.444
H37Rv_KO_Rv1272	-0.71	-0.795
H37Rv_KO_SugABC	-0.066	0.784
H37Rv_KO_MbtN	-0.487	-0.111
Trans05	-0.301	-0.525
macrophage_unactivated	0.698	0.486
IL1	-0.133	0.516
Rapamycin	0.249	0.252
Tcell	0.156	0.075
GMCSF	0.573	0.887
IFNab	0.221	-0.024
IFNg	0.174	-0.168
IFNg_GMCSF1	-0.214	0.119
Rv1432_day32	0.305	-0.061
Rv1565c_day32	0.938	0.91
secA2_input	0.066	-0.982
delta_Rv3594	0.278	0.444
delta_Rv3717	0.576	0.839
delta_Rv3811	0.247	-0.016
delta_Rv0954	1.28	0.41
PonA1	1.09	0.802
EccD1_KO	0.148	0.474
EspI_KO	0.359	-0.048
PE35_KO	-0.099	0.592
PPE68_KO	0.154	0.262
glycerol2	0.633	0.535
lignocerate	0.017	0.53
oleate	0.645	0.509
phosphatidylcholine	0.426	0.609
acetate	0.175	0.206
glucAc	0.216	0.156
Rv0950ko	0.051	0.28
Rv1096ko	0.271	1.071
Rv3684ko	0.95	0.717
delta_otsA_trehalose	-0.165	-0.538