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 Rv1862/adhA:

update plot	correlation	link to info on gene
Rv2281/pitB	(cc=0.5779)	info on Rv2281/pitB
Rv3780/-	(cc=0.5512)	info on Rv3780/-
Rv1725c/-	(cc=0.5347)	info on Rv1725c/-
Rv0278c/PE_PGRS3	(cc=0.5191)	info on Rv0278c/PE_PGRS3
Rv0264c/-	(cc=0.5032)	info on Rv0264c/-
Rv0207c/-	(cc=0.5)	info on Rv0207c/-
Rv2756c/hsdM	(cc=0.4918)	info on Rv2756c/hsdM
Rv1808/PPE32	(cc=0.4905)	info on Rv1808/PPE32
Rv0945/-	(cc=0.4799)	info on Rv0945/-
Rv2802c/-	(cc=0.4779)	info on Rv2802c/-

Correlation of Rv1862/adhA with Rv2281/pitB

Normalized LFCs for Rv1862/adhA:
(description and provenance of datasets)

	Rv1862/adhA	Rv2281/pitB
Fe_supp_jason_reseq	-0.481	0.223
low_pH_jason_reseq	-0.748	-0.343
NO_jason_reseq	-0.121	0.215
B6_jason_reseq	-0.206	0.28
MHCII_jason_reseq	-0.798	-0.784
Isoniazid02	0.611	-1.67
Rifampicin4	0.861	0.458
Ethambutol3	0.308	0.555
Meropenem3	0.31	-0.641
Vancomycin16	0.491	-0.584
Rv2680_day32	0.335	0.336
H37Rv_KO_MarP	0.095	-0.325
hypoxia_3wks	0.06	-0.191
hypoxia_6wks	0.094	-0.1
glycerol	1.059	0.171
cholesterol	0.697	0.215
AJ	0.027	0.482
Bibs02	0.184	0.155
Bibs02c	0.095	0.0
BL6	0.678	0.69
BL6a	0.313	0.469
BXD01	0.192	0.193
BXD010	0.302	0.456
BXD011	0.704	0.591
BXD03	-0.16	-0.234
BXD04	-0.406	-0.139
BXD05	0.239	0.28
BXD06	0.302	0.541
BXD07	0.491	0.643
BXD08	0.301	0.952
BXD09	0.312	1.115
CAST	-0.082	0.27
CCcont	0.555	0.588
DS01	0.654	0.69
DS02	-0.451	0.605
DS04	1.044	-0.419
DS0c	0.751	-0.614
GP01	0.104	0.147
GP02	1.94	1.022
GP0c	0.138	-0.429
NOD	0.296	0.298
NZO	0.023	0.834
PWK	-0.257	0.068
H37Rv_KO_CtpC	0.507	0.165
H37Rv_KO_CtpD	0.481	0.499
H37Rv_KO_Rv1272	0.724	0.097
H37Rv_KO_SugABC	0.451	0.673
H37Rv_KO_MbtN	0.313	-0.316
Trans05	0.271	0.515
macrophage_unactivated	0.748	0.622
IL1	-0.317	0.35
Rapamycin	1.2	0.052
Tcell	0.117	-0.482
GMCSF	-0.04	-0.29
IFNab	0.342	0.051
IFNg	0.019	0.567
IFNg_GMCSF1	0.204	-0.465
Rv1432_day32	0.076	0.231
Rv1565c_day32	0.377	-0.106
secA2_input	-0.257	0.277
delta_Rv3594	0.054	0.34
delta_Rv3717	-0.247	-0.468
delta_Rv3811	0.199	-1.184
delta_Rv0954	0.332	-0.028
PonA1	-0.635	0.299
EccD1_KO	0.539	-0.164
EspI_KO	-0.043	-0.682
PE35_KO	0.236	0.14
PPE68_KO	0.189	0.304
glycerol2	1.471	1.481
lignocerate	1.774	2.191
oleate	0.601	-0.084
phosphatidylcholine	1.529	1.867
acetate	1.348	2.364
glucAc	1.647	2.339
Rv0950ko	-0.048	0.066
Rv1096ko	0.422	0.383
Rv3684ko	-0.206	-0.789
delta_otsA_trehalose	-1.162	-2.033