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 Rv3104c/-:

update plot	correlation	link to info on gene
Rv1128c/-	(cc=0.4738)	info on Rv1128c/-
Rv1752/-	(cc=0.4619)	info on Rv1752/-
Rv0778/cyp126	(cc=0.4422)	info on Rv0778/cyp126
Rv0587/yrbE2A	(cc=0.4378)	info on Rv0587/yrbE2A
Rv3857c/-	(cc=0.4356)	info on Rv3857c/-
Rv3779/-	(cc=0.4352)	info on Rv3779/-
Rv1533/-	(cc=0.434)	info on Rv1533/-
Rv2824c/-	(cc=0.4263)	info on Rv2824c/-
Rv0380c/-	(cc=0.4129)	info on Rv0380c/-
Rv0619/galTb	(cc=0.4119)	info on Rv0619/galTb

Correlation of Rv3104c/- with Rv2824c/-

Normalized LFCs for Rv3104c/-:
(description and provenance of datasets)

	Rv3104c/-	Rv2824c/-
Fe_supp_jason_reseq	1.44	-0.028
low_pH_jason_reseq	-0.574	-0.898
NO_jason_reseq	-0.704	-0.194
B6_jason_reseq	-0.434	-0.418
MHCII_jason_reseq	0.884	-1.175
Isoniazid02	0.127	0.089
Rifampicin4	0.192	-0.634
Ethambutol3	-0.592	-0.038
Meropenem3	0.458	-0.012
Vancomycin16	-0.175	0.186
Rv2680_day32	-0.354	-0.603
H37Rv_KO_MarP	0.765	0.394
hypoxia_3wks	1.188	0.969
hypoxia_6wks	1.566	1.66
glycerol	0.278	0.699
cholesterol	-0.34	-0.237
AJ	-0.445	-0.266
Bibs02	-0.16	-0.768
Bibs02c	-0.42	-0.324
BL6	0.101	0.774
BL6a	0.344	0.377
BXD01	0.493	0.675
BXD010	0.367	0.691
BXD011	0.358	0.654
BXD03	0.073	0.274
BXD04	1.237	0.402
BXD05	1.169	0.946
BXD06	0.24	0.878
BXD07	0.855	0.829
BXD08	0.73	0.101
BXD09	0.447	0.678
CAST	-0.384	-0.601
CCcont	0.608	0.494
DS01	-0.226	0.099
DS02	0.287	-0.063
DS04	-0.829	0.559
DS0c	0.679	0.016
GP01	-0.313	-0.363
GP02	-0.321	0.359
GP0c	0.359	0.082
NOD	0.905	-0.116
NZO	0.027	-0.014
PWK	0.081	0.149
H37Rv_KO_CtpC	0.723	0.753
H37Rv_KO_CtpD	1.029	0.931
H37Rv_KO_Rv1272	-0.168	-0.184
H37Rv_KO_SugABC	0.33	0.408
H37Rv_KO_MbtN	0.11	0.078
Trans05	0.131	0.699
macrophage_unactivated	0.464	-0.085
IL1	0.768	0.139
Rapamycin	1.467	0.0
Tcell	0.652	0.541
GMCSF	0.409	0.106
IFNab	0.348	-0.408
IFNg	0.35	0.278
IFNg_GMCSF1	0.606	-0.022
Rv1432_day32	0.789	0.424
Rv1565c_day32	-1.671	-0.336
secA2_input	0.611	-0.042
delta_Rv3594	0.211	-0.112
delta_Rv3717	0.0	-0.552
delta_Rv3811	-0.126	-0.455
delta_Rv0954	0.981	-0.346
PonA1	0.233	-0.531
EccD1_KO	-0.927	-1.095
EspI_KO	0.063	-0.157
PE35_KO	-0.747	0.105
PPE68_KO	-0.682	0.333
glycerol2	-0.46	-0.074
lignocerate	-0.342	0.347
oleate	-0.323	-0.237
phosphatidylcholine	-0.287	0.22
acetate	-0.642	0.113
glucAc	-0.365	0.07
Rv0950ko	0.582	-0.045
Rv1096ko	0.431	-0.44
Rv3684ko	0.422	-0.049
delta_otsA_trehalose	-1.37	-0.338