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 Rv1817/-:

update plot	correlation	link to info on gene
Rv2113/-	(cc=0.8479)	info on Rv2113/-
Rv0453/PPE11	(cc=0.8091)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7965)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.7829)	info on Rv2822c/-
Rv0159c/PE3	(cc=0.7688)	info on Rv0159c/PE3
Rv3815c/-	(cc=0.7673)	info on Rv3815c/-
Rv3862c/whiB6	(cc=0.5436)	info on Rv3862c/whiB6
Rv2339/mmpL9	(cc=0.5212)	info on Rv2339/mmpL9
Rv3685c/cyp137	(cc=0.5029)	info on Rv3685c/cyp137
Rv2389c/rpfD	(cc=0.5017)	info on Rv2389c/rpfD

Correlation of Rv1817/- with Rv2113/-

Normalized LFCs for Rv1817/-:
(description and provenance of datasets)

	Rv1817/-	Rv2113/-
Fe_supp_jason_reseq	-0.223	0.922
low_pH_jason_reseq	-0.388	-1.379
NO_jason_reseq	-0.714	-0.559
B6_jason_reseq	-0.232	-1.249
MHCII_jason_reseq	0.326	-0.531
Isoniazid02	0.215	-1.043
Rifampicin4	0.0	0.406
Ethambutol3	0.612	0.657
Meropenem3	0.316	-0.462
Vancomycin16	-0.04	-0.231
Rv2680_day32	-0.437	-0.825
H37Rv_KO_MarP	-0.186	0.159
hypoxia_3wks	0.116	-0.012
hypoxia_6wks	-0.203	-0.568
glycerol	0.604	0.237
cholesterol	0.241	-0.405
AJ	-0.311	0.356
Bibs02	0.738	-0.372
Bibs02c	0.358	-0.209
BL6	-0.327	0.418
BL6a	-0.133	0.169
BXD01	0.177	-0.106
BXD010	-0.209	-0.113
BXD011	0.092	0.753
BXD03	-0.113	0.123
BXD04	-0.103	-0.166
BXD05	-0.219	0.301
BXD06	0.007	0.224
BXD07	-0.344	0.171
BXD08	0.091	0.265
BXD09	-0.331	0.103
CAST	0.22	-0.828
CCcont	-0.371	0.169
DS01	0.453	-0.335
DS02	0.334	0.098
DS04	0.332	-0.218
DS0c	0.409	0.11
GP01	-0.077	0.072
GP02	0.301	-0.087
GP0c	-0.088	0.142
NOD	0.441	-0.404
NZO	0.069	-0.604
PWK	0.068	-0.409
H37Rv_KO_CtpC	0.111	0.148
H37Rv_KO_CtpD	0.178	0.72
H37Rv_KO_Rv1272	1.0	0.551
H37Rv_KO_SugABC	-0.144	1.132
H37Rv_KO_MbtN	0.43	0.42
Trans05	1.011	0.939
macrophage_unactivated	1.588	1.143
IL1	2.201	2.886
Rapamycin	2.317	3.167
Tcell	-4.923	-6.0
GMCSF	2.26	2.756
IFNab	1.886	2.663
IFNg	2.397	2.905
IFNg_GMCSF1	2.385	2.963
Rv1432_day32	0.096	0.322
Rv1565c_day32	-0.156	1.531
secA2_input	-0.434	0.128
delta_Rv3594	0.0	-0.337
delta_Rv3717	-0.028	-0.154
delta_Rv3811	0.28	-0.312
delta_Rv0954	0.142	0.181
PonA1	-0.059	-0.268
EccD1_KO	0.687	0.148
EspI_KO	0.359	0.222
PE35_KO	0.63	-0.286
PPE68_KO	0.56	-0.147
glycerol2	0.085	0.894
lignocerate	-0.069	0.616
oleate	0.386	1.331
phosphatidylcholine	0.239	0.999
acetate	-0.156	0.342
glucAc	-0.167	-0.082
Rv0950ko	0.13	0.25
Rv1096ko	-0.392	-0.13
Rv3684ko	-0.102	-0.233
delta_otsA_trehalose	-0.085	0.537