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 Rv1558/-:

update plot	correlation	link to info on gene
Rv3633/-	(cc=0.5149)	info on Rv3633/-
Rv2972c/-	(cc=0.4966)	info on Rv2972c/-
Rv0726c/-	(cc=0.439)	info on Rv0726c/-
Rv3312A/-	(cc=0.4323)	info on Rv3312A/-
Rv3451/cut3	(cc=0.4274)	info on Rv3451/cut3
Rv1719/-	(cc=0.3898)	info on Rv1719/-
Rv3826/fadD23	(cc=0.3817)	info on Rv3826/fadD23
Rv0873/fadE10	(cc=0.3783)	info on Rv0873/fadE10
Rv0530/-	(cc=0.3752)	info on Rv0530/-
Rv2459/-	(cc=0.373)	info on Rv2459/-

Correlation of Rv1558/- with Rv0726c/-

Normalized LFCs for Rv1558/-:
(description and provenance of datasets)

	Rv1558/-	Rv0726c/-
Fe_supp_jason_reseq	0.248	-0.248
low_pH_jason_reseq	-1.022	-0.494
NO_jason_reseq	0.058	-0.648
B6_jason_reseq	0.883	0.22
MHCII_jason_reseq	1.104	0.199
Isoniazid02	-0.687	0.1
Rifampicin4	0.682	0.276
Ethambutol3	-0.305	-0.088
Meropenem3	1.242	0.419
Vancomycin16	-0.159	0.024
Rv2680_day32	0.042	-1.212
H37Rv_KO_MarP	0.144	0.209
hypoxia_3wks	-0.287	0.522
hypoxia_6wks	-0.507	0.516
glycerol	-0.503	-0.717
cholesterol	-0.504	-0.377
AJ	0.462	0.333
Bibs02	0.487	-0.421
Bibs02c	0.649	0.12
BL6	-0.091	0.869
BL6a	0.317	0.647
BXD01	-0.044	0.736
BXD010	0.523	0.61
BXD011	0.149	1.075
BXD03	0.256	-0.108
BXD04	0.326	0.794
BXD05	-0.067	0.998
BXD06	0.24	0.664
BXD07	0.107	0.573
BXD08	0.218	0.987
BXD09	0.189	0.326
CAST	0.023	1.016
CCcont	-0.421	0.103
DS01	0.645	0.515
DS02	0.501	0.644
DS04	0.479	1.15
DS0c	1.358	0.555
GP01	0.343	-0.006
GP02	0.554	0.847
GP0c	-0.201	-0.494
NOD	-0.436	0.203
NZO	0.462	-0.431
PWK	0.311	0.492
H37Rv_KO_CtpC	0.312	-0.351
H37Rv_KO_CtpD	0.568	1.462
H37Rv_KO_Rv1272	-1.188	0.143
H37Rv_KO_SugABC	-1.189	0.467
H37Rv_KO_MbtN	0.35	-0.522
Trans05	-0.949	0.31
macrophage_unactivated	0.098	0.0
IL1	0.409	-0.747
Rapamycin	0.543	-0.325
Tcell	0.186	0.463
GMCSF	0.399	0.343
IFNab	-0.269	-0.432
IFNg	0.123	-0.361
IFNg_GMCSF1	0.135	0.82
Rv1432_day32	-0.623	-0.503
Rv1565c_day32	-3.116	-1.884
secA2_input	-0.122	-0.506
delta_Rv3594	-0.099	0.653
delta_Rv3717	-0.186	-0.272
delta_Rv3811	-0.335	0.916
delta_Rv0954	0.647	0.845
PonA1	0.9	0.781
EccD1_KO	-0.585	-0.556
EspI_KO	0.348	0.231
PE35_KO	0.292	-0.298
PPE68_KO	0.87	-0.301
glycerol2	0.397	0.346
lignocerate	0.385	0.139
oleate	0.72	1.18
phosphatidylcholine	0.469	0.766
acetate	-0.336	-0.63
glucAc	0.241	-0.97
Rv0950ko	0.552	0.145
Rv1096ko	-0.181	0.205
Rv3684ko	0.095	-0.504
delta_otsA_trehalose	1.305	2.046