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 Rv3724B/cut5b:

update plot	correlation	link to info on gene
Rv1526c/-	(cc=0.4944)	info on Rv1526c/-
Rv0469/umaA	(cc=0.4815)	info on Rv0469/umaA
Rv2730/-	(cc=0.4793)	info on Rv2730/-
Rv3742c/-	(cc=0.4701)	info on Rv3742c/-
Rv3232c/ppk2	(cc=0.4673)	info on Rv3232c/ppk2
Rv2519/PE26	(cc=0.4658)	info on Rv2519/PE26
Rv3142c/-	(cc=0.4546)	info on Rv3142c/-
Rv1213/glgC	(cc=0.4478)	info on Rv1213/glgC
Rv2568c/-	(cc=0.4466)	info on Rv2568c/-
Rv3377c/-	(cc=0.4383)	info on Rv3377c/-

Correlation of Rv3724B/cut5b with Rv1526c/-

Normalized LFCs for Rv3724B/cut5b:
(description and provenance of datasets)

	Rv3724B/cut5b	Rv1526c/-
Fe_supp_jason_reseq	0.178	0.082
low_pH_jason_reseq	-0.177	0.043
NO_jason_reseq	-0.168	0.331
B6_jason_reseq	-0.752	-2.248
MHCII_jason_reseq	-0.233	-1.614
Isoniazid02	-0.696	0.047
Rifampicin4	-0.772	-0.325
Ethambutol3	0.236	-0.212
Meropenem3	-0.237	-0.165
Vancomycin16	-1.186	-0.133
Rv2680_day32	-0.511	-0.548
H37Rv_KO_MarP	0.533	1.37
hypoxia_3wks	-0.622	-0.558
hypoxia_6wks	-0.035	0.0
glycerol	-0.08	0.243
cholesterol	-0.138	-0.038
AJ	-0.03	0.225
Bibs02	-0.699	-0.415
Bibs02c	0.341	0.344
BL6	-0.016	2.032
BL6a	0.138	1.277
BXD01	0.482	1.115
BXD010	1.04	1.082
BXD011	-0.078	2.02
BXD03	0.102	1.063
BXD04	-0.092	0.426
BXD05	0.242	1.058
BXD06	0.507	0.967
BXD07	0.138	1.868
BXD08	-0.166	0.575
BXD09	0.237	1.249
CAST	0.0	0.707
CCcont	0.301	1.423
DS01	-0.015	0.633
DS02	-0.369	0.748
DS04	-1.122	0.402
DS0c	0.803	-0.295
GP01	0.536	0.727
GP02	0.224	1.017
GP0c	0.034	1.754
NOD	-0.075	1.154
NZO	0.302	0.1
PWK	0.242	-0.156
H37Rv_KO_CtpC	0.653	1.462
H37Rv_KO_CtpD	1.124	1.973
H37Rv_KO_Rv1272	1.328	2.07
H37Rv_KO_SugABC	0.701	1.981
H37Rv_KO_MbtN	-0.063	0.479
Trans05	0.694	1.657
macrophage_unactivated	-0.082	0.71
IL1	-0.077	0.095
Rapamycin	-0.322	0.648
Tcell	0.371	0.909
GMCSF	-0.114	0.594
IFNab	-0.514	0.239
IFNg	-1.026	1.056
IFNg_GMCSF1	-0.217	0.05
Rv1432_day32	0.0	-0.87
Rv1565c_day32	0.491	-0.291
secA2_input	-0.025	-0.482
delta_Rv3594	0.107	0.895
delta_Rv3717	-0.355	0.029
delta_Rv3811	0.983	1.17
delta_Rv0954	0.152	0.652
PonA1	0.703	1.392
EccD1_KO	-0.053	0.835
EspI_KO	0.18	0.967
PE35_KO	-0.143	0.989
PPE68_KO	-0.106	0.95
glycerol2	-0.406	0.376
lignocerate	0.027	1.333
oleate	-1.158	-1.157
phosphatidylcholine	-0.499	0.758
acetate	-0.529	1.403
glucAc	0.105	1.533
Rv0950ko	0.482	-0.265
Rv1096ko	-0.365	-0.407
Rv3684ko	0.029	-0.704
delta_otsA_trehalose	0.795	1.158