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 Rv2176/pknL:

update plot	correlation	link to info on gene
Rv2004c/-	(cc=0.5634)	info on Rv2004c/-
Rv0876c/-	(cc=0.5121)	info on Rv0876c/-
Rv0020c/fhaA	(cc=0.5078)	info on Rv0020c/fhaA
Rv0016c/pbpA	(cc=0.4982)	info on Rv0016c/pbpA
Rv1199c/-	(cc=0.4954)	info on Rv1199c/-
Rv2512c/-	(cc=0.4911)	info on Rv2512c/-
Rv1917c/PPE34	(cc=0.4784)	info on Rv1917c/PPE34
Rv0017c/rodA	(cc=0.4757)	info on Rv0017c/rodA
Rv2148c/-	(cc=0.469)	info on Rv2148c/-
Rv0867c/rpfA	(cc=0.4612)	info on Rv0867c/rpfA

Correlation of Rv2176/pknL with Rv2004c/-

Normalized LFCs for Rv2176/pknL:
(description and provenance of datasets)

	Rv2176/pknL	Rv2004c/-
Fe_supp_jason_reseq	0.42	0.655
low_pH_jason_reseq	0.315	0.592
NO_jason_reseq	0.617	0.0
B6_jason_reseq	0.06	0.526
MHCII_jason_reseq	-0.018	2.331
Isoniazid02	-0.674	-1.48
Rifampicin4	-0.999	-1.4
Ethambutol3	-2.089	-1.418
Meropenem3	-0.052	-1.157
Vancomycin16	-0.883	-1.149
Rv2680_day32	-0.51	0.608
H37Rv_KO_MarP	-2.077	-0.936
hypoxia_3wks	0.0	0.969
hypoxia_6wks	0.142	0.236
glycerol	-0.373	2.262
cholesterol	0.21	1.492
AJ	0.158	0.598
Bibs02	1.285	0.898
Bibs02c	1.299	2.801
BL6	0.085	0.982
BL6a	0.983	2.218
BXD01	0.368	1.666
BXD010	0.506	0.372
BXD011	0.26	0.896
BXD03	-0.8	0.592
BXD04	0.1	1.385
BXD05	-0.47	1.344
BXD06	0.073	0.995
BXD07	-0.539	1.665
BXD08	0.637	2.226
BXD09	-0.146	0.958
CAST	-0.312	-0.928
CCcont	0.18	1.202
DS01	1.591	2.281
DS02	1.416	1.435
DS04	2.264	2.117
DS0c	2.077	1.788
GP01	1.011	1.367
GP02	-0.359	1.104
GP0c	-0.24	0.996
NOD	0.843	-0.905
NZO	-0.058	-1.065
PWK	1.155	-1.189
H37Rv_KO_CtpC	0.957	1.486
H37Rv_KO_CtpD	0.853	1.305
H37Rv_KO_Rv1272	0.808	2.101
H37Rv_KO_SugABC	0.92	0.94
H37Rv_KO_MbtN	0.302	2.096
Trans05	1.104	2.198
macrophage_unactivated	0.546	1.158
IL1	-0.077	-0.872
Rapamycin	-0.335	0.114
Tcell	0.251	0.58
GMCSF	-0.069	0.38
IFNab	-0.16	0.834
IFNg	1.09	0.198
IFNg_GMCSF1	-0.811	-0.779
Rv1432_day32	-0.763	1.51
Rv1565c_day32	0.0	0.0
secA2_input	-0.377	-0.294
delta_Rv3594	0.545	-0.171
delta_Rv3717	0.39	0.162
delta_Rv3811	0.269	-0.123
delta_Rv0954	-1.368	-1.835
PonA1	-2.68	-1.597
EccD1_KO	0.457	-0.414
EspI_KO	0.519	0.485
PE35_KO	0.405	0.572
PPE68_KO	0.102	1.254
glycerol2	0.241	0.671
lignocerate	0.449	0.381
oleate	-1.664	-1.184
phosphatidylcholine	0.723	0.203
acetate	0.09	0.106
glucAc	0.161	0.324
Rv0950ko	-0.811	-0.087
Rv1096ko	-1.408	0.721
Rv3684ko	-0.943	0.0
delta_otsA_trehalose	0.158	0.353