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 Rv0446c/-:

update plot	correlation	link to info on gene
Rv3636/-	(cc=0.474)	info on Rv3636/-
Rv2857c/-	(cc=0.4455)	info on Rv2857c/-
Rv1417/-	(cc=0.4388)	info on Rv1417/-
Rv2218/lipA	(cc=0.4315)	info on Rv2218/lipA
Rv2234/ptpA	(cc=0.4282)	info on Rv2234/ptpA
Rv1496/-	(cc=0.4016)	info on Rv1496/-
Rv1269c/-	(cc=0.3973)	info on Rv1269c/-
Rv2877c/-	(cc=0.3924)	info on Rv2877c/-
Rv3379c/dxs2	(cc=0.3904)	info on Rv3379c/dxs2
Rv0575c/-	(cc=0.387)	info on Rv0575c/-

Correlation of Rv0446c/- with Rv3636/-

Normalized LFCs for Rv0446c/-:
(description and provenance of datasets)

	Rv0446c/-	Rv3636/-
Fe_supp_jason_reseq	1.051	0.559
low_pH_jason_reseq	0.186	-0.032
NO_jason_reseq	-0.142	1.391
B6_jason_reseq	-0.178	0.093
MHCII_jason_reseq	0.678	0.991
Isoniazid02	-0.198	0.288
Rifampicin4	-0.1	0.707
Ethambutol3	0.202	0.136
Meropenem3	0.075	1.744
Vancomycin16	0.072	0.875
Rv2680_day32	-0.628	-2.621
H37Rv_KO_MarP	0.392	0.831
hypoxia_3wks	0.339	0.315
hypoxia_6wks	-0.169	-0.453
glycerol	-0.465	1.059
cholesterol	-0.203	-0.057
AJ	-0.183	0.977
Bibs02	-0.673	-0.766
Bibs02c	0.023	-0.418
BL6	0.684	-0.488
BL6a	-0.168	-0.284
BXD01	-0.014	0.873
BXD010	-0.139	0.852
BXD011	-0.234	0.591
BXD03	-0.284	-0.509
BXD04	0.585	-0.012
BXD05	0.541	0.331
BXD06	-0.029	0.349
BXD07	0.171	0.864
BXD08	0.036	0.585
BXD09	0.233	0.336
CAST	-0.224	-0.232
CCcont	-0.227	-0.231
DS01	-0.344	0.195
DS02	-1.185	0.274
DS04	-0.5	0.357
DS0c	-0.385	-0.385
GP01	-0.175	-0.386
GP02	0.672	0.451
GP0c	-0.119	0.798
NOD	-1.103	-1.362
NZO	0.022	1.445
PWK	0.053	1.017
H37Rv_KO_CtpC	-0.755	0.246
H37Rv_KO_CtpD	0.958	0.36
H37Rv_KO_Rv1272	-0.103	0.909
H37Rv_KO_SugABC	0.613	0.206
H37Rv_KO_MbtN	0.276	0.407
Trans05	0.021	1.694
macrophage_unactivated	0.224	-0.041
IL1	0.021	0.62
Rapamycin	0.322	0.979
Tcell	0.094	0.492
GMCSF	0.349	0.301
IFNab	0.378	-0.248
IFNg	1.09	0.853
IFNg_GMCSF1	0.135	1.295
Rv1432_day32	-0.498	-0.18
Rv1565c_day32	0.374	0.329
secA2_input	-0.518	-0.675
delta_Rv3594	-1.002	-1.104
delta_Rv3717	-0.638	-0.106
delta_Rv3811	-0.836	-0.462
delta_Rv0954	0.631	0.49
PonA1	-0.384	-0.021
EccD1_KO	-0.191	-0.335
EspI_KO	0.248	0.251
PE35_KO	-0.073	0.172
PPE68_KO	-0.582	0.096
glycerol2	-0.011	0.097
lignocerate	0.253	-0.077
oleate	-0.101	0.62
phosphatidylcholine	-0.066	0.06
acetate	-0.482	-0.432
glucAc	-0.339	-0.582
Rv0950ko	0.434	0.938
Rv1096ko	0.694	2.129
Rv3684ko	0.442	1.634
delta_otsA_trehalose	-0.645	-1.138