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 Rv0604/lpqO:

update plot	correlation	link to info on gene
Rv2879c/-	(cc=0.519)	info on Rv2879c/-
Rv1249c/-	(cc=0.4964)	info on Rv1249c/-
Rv1442/bisC	(cc=0.4954)	info on Rv1442/bisC
Rv3532/PPE61	(cc=0.4866)	info on Rv3532/PPE61
Rv0302/-	(cc=0.4756)	info on Rv0302/-
Rv2007c/fdxA	(cc=0.4718)	info on Rv2007c/fdxA
Rv2880c/-	(cc=0.4691)	info on Rv2880c/-
Rv0015c/pknA	(cc=0.4678)	info on Rv0015c/pknA
Rv0269c/-	(cc=0.4656)	info on Rv0269c/-
Rv0061c/-	(cc=0.4604)	info on Rv0061c/-

Correlation of Rv0604/lpqO with Rv3532/PPE61

Normalized LFCs for Rv0604/lpqO:
(description and provenance of datasets)

	Rv0604/lpqO	Rv3532/PPE61
Fe_supp_jason_reseq	1.159	-0.058
low_pH_jason_reseq	-1.474	-0.79
NO_jason_reseq	-2.195	-0.194
B6_jason_reseq	0.798	0.706
MHCII_jason_reseq	1.287	0.622
Isoniazid02	0.038	0.501
Rifampicin4	0.347	0.019
Ethambutol3	-0.17	0.798
Meropenem3	0.048	0.187
Vancomycin16	0.0	0.204
Rv2680_day32	-0.525	-0.116
H37Rv_KO_MarP	0.116	0.203
hypoxia_3wks	0.53	0.096
hypoxia_6wks	-0.507	-0.129
glycerol	1.27	0.334
cholesterol	0.077	0.284
AJ	0.729	0.05
Bibs02	1.249	0.313
Bibs02c	0.896	0.371
BL6	0.144	0.12
BL6a	0.027	-0.014
BXD01	0.39	-0.209
BXD010	-0.118	-0.409
BXD011	-0.94	0.005
BXD03	-0.115	0.054
BXD04	-1.037	-0.004
BXD05	0.089	0.371
BXD06	-0.78	-0.348
BXD07	-0.46	-0.241
BXD08	0.509	-0.537
BXD09	-0.416	-0.257
CAST	-0.112	0.452
CCcont	0.098	-0.011
DS01	0.731	0.435
DS02	0.684	0.317
DS04	0.839	0.357
DS0c	0.404	0.731
GP01	0.0	0.479
GP02	-0.262	0.504
GP0c	-0.101	-0.254
NOD	-0.921	0.049
NZO	0.118	0.238
PWK	-0.124	0.267
H37Rv_KO_CtpC	-1.291	0.344
H37Rv_KO_CtpD	-0.532	0.176
H37Rv_KO_Rv1272	-1.06	0.169
H37Rv_KO_SugABC	-1.802	0.239
H37Rv_KO_MbtN	-0.819	-0.361
Trans05	0.462	-0.31
macrophage_unactivated	1.18	-0.417
IL1	0.027	-0.427
Rapamycin	-0.792	-0.282
Tcell	-0.274	-0.156
GMCSF	0.14	-0.259
IFNab	-0.342	0.203
IFNg	-1.085	-0.086
IFNg_GMCSF1	2.124	0.132
Rv1432_day32	1.395	1.514
Rv1565c_day32	1.058	0.286
secA2_input	-0.221	-0.291
delta_Rv3594	-0.857	-0.427
delta_Rv3717	-1.05	-0.205
delta_Rv3811	-1.689	-0.346
delta_Rv0954	-0.724	-0.275
PonA1	-2.328	-0.441
EccD1_KO	0.506	-0.145
EspI_KO	-0.24	-0.465
PE35_KO	0.175	-0.23
PPE68_KO	0.637	-0.221
glycerol2	0.726	0.907
lignocerate	1.142	0.6
oleate	1.353	0.818
phosphatidylcholine	1.452	0.605
acetate	0.843	0.038
glucAc	0.631	0.0
Rv0950ko	0.799	0.317
Rv1096ko	0.124	0.015
Rv3684ko	0.665	-0.046
delta_otsA_trehalose	1.318	1.375