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 Rv0728c/serA2:

update plot	correlation	link to info on gene
Rv2330c/lppP	(cc=0.5127)	info on Rv2330c/lppP
Rv2451/-	(cc=0.4823)	info on Rv2451/-
Rv3584/lpqE	(cc=0.4608)	info on Rv3584/lpqE
Rv1482c/-	(cc=0.4543)	info on Rv1482c/-
Rv3105c/prfB	(cc=0.448)	info on Rv3105c/prfB
Rv3198A/-	(cc=0.4478)	info on Rv3198A/-
Rv2970A/-	(cc=0.4374)	info on Rv2970A/-
Rv2736c/recX	(cc=0.4351)	info on Rv2736c/recX
Rv0463/-	(cc=0.4207)	info on Rv0463/-
Rv1525/wbbL2	(cc=0.4139)	info on Rv1525/wbbL2

Correlation of Rv0728c/serA2 with Rv3198A/-

Normalized LFCs for Rv0728c/serA2:
(description and provenance of datasets)

	Rv0728c/serA2	Rv3198A/-
Fe_supp_jason_reseq	0.584	0.079
low_pH_jason_reseq	-0.744	-0.888
NO_jason_reseq	-0.494	-0.562
B6_jason_reseq	-0.184	-0.557
MHCII_jason_reseq	-0.151	-0.498
Isoniazid02	0.068	0.732
Rifampicin4	0.349	-0.682
Ethambutol3	0.0	0.316
Meropenem3	1.656	0.343
Vancomycin16	0.822	-0.146
Rv2680_day32	-0.252	-0.341
H37Rv_KO_MarP	0.246	-0.056
hypoxia_3wks	0.387	-0.08
hypoxia_6wks	0.679	0.349
glycerol	-0.471	-1.66
cholesterol	-0.371	-0.806
AJ	0.282	-0.015
Bibs02	-0.832	-0.179
Bibs02c	0.42	0.252
BL6	0.407	-0.255
BL6a	0.336	0.079
BXD01	0.242	0.208
BXD010	0.989	0.107
BXD011	1.865	0.124
BXD03	0.127	0.567
BXD04	0.472	0.901
BXD05	0.818	-0.076
BXD06	0.666	0.178
BXD07	0.462	0.253
BXD08	0.752	0.421
BXD09	0.624	0.522
CAST	0.342	-0.167
CCcont	-0.076	0.092
DS01	-0.26	0.279
DS02	-0.969	0.178
DS04	-0.707	-0.03
DS0c	-0.625	0.423
GP01	-0.703	-0.331
GP02	-1.195	-2.099
GP0c	-0.776	-0.014
NOD	-0.456	-0.205
NZO	0.538	-0.355
PWK	-0.151	0.247
H37Rv_KO_CtpC	0.896	-0.265
H37Rv_KO_CtpD	-1.949	-0.187
H37Rv_KO_Rv1272	0.626	0.468
H37Rv_KO_SugABC	0.361	0.75
H37Rv_KO_MbtN	0.712	0.802
Trans05	0.327	0.442
macrophage_unactivated	0.0	0.432
IL1	0.056	0.386
Rapamycin	0.678	0.838
Tcell	0.244	-0.235
GMCSF	0.116	1.215
IFNab	0.0	0.378
IFNg	0.361	0.176
IFNg_GMCSF1	0.71	0.575
Rv1432_day32	1.709	0.506
Rv1565c_day32	0.392	-0.044
secA2_input	0.044	0.186
delta_Rv3594	-1.418	-0.239
delta_Rv3717	-0.603	-0.452
delta_Rv3811	-0.931	-1.016
delta_Rv0954	-0.848	-0.382
PonA1	0.07	-0.184
EccD1_KO	0.026	0.345
EspI_KO	0.242	0.103
PE35_KO	-0.166	-0.172
PPE68_KO	-0.624	-0.49
glycerol2	0.242	0.86
lignocerate	0.407	0.712
oleate	0.047	0.506
phosphatidylcholine	0.113	0.794
acetate	-0.113	-0.183
glucAc	0.116	0.8
Rv0950ko	0.078	1.01
Rv1096ko	-0.133	0.0
Rv3684ko	-0.413	0.131
delta_otsA_trehalose	-0.68	-0.097