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 Rv2300c/-:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.5432)	info on Rv3738c/PPE66
Rv2497c/bkdA	(cc=0.4583)	info on Rv2497c/bkdA
Rv3485c/-	(cc=0.4561)	info on Rv3485c/-
Rv0830/-	(cc=0.4523)	info on Rv0830/-
Rv1141c/echA11	(cc=0.4476)	info on Rv1141c/echA11
Rv0872c/PE_PGRS15	(cc=0.439)	info on Rv0872c/PE_PGRS15
Rv3435c/-	(cc=0.4362)	info on Rv3435c/-
Rv2345/-	(cc=0.4342)	info on Rv2345/-
Rv1153c/omt	(cc=0.43)	info on Rv1153c/omt
Rv3092c/-	(cc=0.4259)	info on Rv3092c/-

Correlation of Rv2300c/- with Rv3738c/PPE66

Normalized LFCs for Rv2300c/-:
(description and provenance of datasets)

	Rv2300c/-	Rv3738c/PPE66
Fe_supp_jason_reseq	-0.223	-0.238
low_pH_jason_reseq	-0.714	-0.192
NO_jason_reseq	0.071	-0.034
B6_jason_reseq	0.016	-0.216
MHCII_jason_reseq	0.209	0.063
Isoniazid02	-0.113	-0.949
Rifampicin4	-0.097	-0.014
Ethambutol3	-0.022	-0.585
Meropenem3	-0.4	-0.751
Vancomycin16	-0.194	-0.825
Rv2680_day32	-1.068	0.525
H37Rv_KO_MarP	-0.078	0.365
hypoxia_3wks	0.171	-0.363
hypoxia_6wks	0.177	-0.716
glycerol	-0.658	-0.75
cholesterol	-0.495	-0.871
AJ	-0.126	-0.491
Bibs02	-0.099	0.042
Bibs02c	0.391	1.031
BL6	0.237	0.475
BL6a	0.194	0.947
BXD01	0.109	0.456
BXD010	0.549	0.395
BXD011	0.467	0.668
BXD03	0.122	0.155
BXD04	0.014	0.142
BXD05	-0.453	0.452
BXD06	0.035	0.191
BXD07	0.259	0.205
BXD08	0.491	0.124
BXD09	0.253	0.225
CAST	0.272	-0.087
CCcont	0.236	0.094
DS01	0.062	-0.044
DS02	-0.076	0.03
DS04	0.169	0.215
DS0c	0.314	0.148
GP01	0.099	0.298
GP02	0.592	1.222
GP0c	-0.056	0.739
NOD	0.234	0.182
NZO	0.513	-0.624
PWK	0.428	0.134
H37Rv_KO_CtpC	0.364	0.718
H37Rv_KO_CtpD	0.696	1.243
H37Rv_KO_Rv1272	1.149	0.297
H37Rv_KO_SugABC	0.374	0.756
H37Rv_KO_MbtN	0.381	0.763
Trans05	0.325	0.529
macrophage_unactivated	0.139	0.496
IL1	0.332	0.605
Rapamycin	0.04	0.178
Tcell	0.029	0.316
GMCSF	0.174	0.356
IFNab	0.121	0.018
IFNg	0.484	-0.128
IFNg_GMCSF1	0.531	-0.057
Rv1432_day32	0.519	0.297
Rv1565c_day32	0.21	-0.046
secA2_input	0.913	0.46
delta_Rv3594	0.095	-0.488
delta_Rv3717	-0.249	-0.881
delta_Rv3811	-0.397	-0.892
delta_Rv0954	-0.649	-0.198
PonA1	-0.321	-0.443
EccD1_KO	0.227	-0.234
EspI_KO	0.465	-0.359
PE35_KO	0.376	-0.327
PPE68_KO	0.118	-0.154
glycerol2	0.738	0.824
lignocerate	0.82	0.927
oleate	1.007	0.953
phosphatidylcholine	0.91	0.975
acetate	0.096	0.076
glucAc	0.207	0.269
Rv0950ko	0.874	0.458
Rv1096ko	0.214	-0.377
Rv3684ko	0.049	-0.269
delta_otsA_trehalose	0.871	1.259