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 Rv2497c/bkdA

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

	Rv2300c/-	Rv2497c/bkdA
Fe_supp_jason_reseq	-0.223	-0.297
low_pH_jason_reseq	-0.714	0.244
NO_jason_reseq	0.071	0.36
B6_jason_reseq	0.016	-1.575
MHCII_jason_reseq	0.209	0.011
Isoniazid02	-0.113	-1.077
Rifampicin4	-0.097	0.263
Ethambutol3	-0.022	-1.058
Meropenem3	-0.4	-0.461
Vancomycin16	-0.194	-1.035
Rv2680_day32	-1.068	-0.473
H37Rv_KO_MarP	-0.078	-0.144
hypoxia_3wks	0.171	0.634
hypoxia_6wks	0.177	-0.578
glycerol	-0.658	-1.842
cholesterol	-0.495	0.311
AJ	-0.126	-0.062
Bibs02	-0.099	0.432
Bibs02c	0.391	0.426
BL6	0.237	0.255
BL6a	0.194	0.666
BXD01	0.109	0.147
BXD010	0.549	0.491
BXD011	0.467	0.476
BXD03	0.122	-0.389
BXD04	0.014	-0.334
BXD05	-0.453	0.528
BXD06	0.035	0.342
BXD07	0.259	0.641
BXD08	0.491	0.118
BXD09	0.253	0.732
CAST	0.272	-1.006
CCcont	0.236	0.444
DS01	0.062	0.238
DS02	-0.076	-0.375
DS04	0.169	0.125
DS0c	0.314	0.644
GP01	0.099	0.682
GP02	0.592	0.178
GP0c	-0.056	0.192
NOD	0.234	-0.218
NZO	0.513	0.103
PWK	0.428	0.503
H37Rv_KO_CtpC	0.364	1.407
H37Rv_KO_CtpD	0.696	0.299
H37Rv_KO_Rv1272	1.149	1.469
H37Rv_KO_SugABC	0.374	1.395
H37Rv_KO_MbtN	0.381	0.21
Trans05	0.325	0.92
macrophage_unactivated	0.139	1.111
IL1	0.332	0.676
Rapamycin	0.04	0.246
Tcell	0.029	0.668
GMCSF	0.174	0.784
IFNab	0.121	0.828
IFNg	0.484	1.053
IFNg_GMCSF1	0.531	0.49
Rv1432_day32	0.519	-0.117
Rv1565c_day32	0.21	-0.542
secA2_input	0.913	0.509
delta_Rv3594	0.095	-0.24
delta_Rv3717	-0.249	0.305
delta_Rv3811	-0.397	-0.214
delta_Rv0954	-0.649	-0.669
PonA1	-0.321	-0.777
EccD1_KO	0.227	-0.51
EspI_KO	0.465	-1.072
PE35_KO	0.376	0.184
PPE68_KO	0.118	0.422
glycerol2	0.738	0.581
lignocerate	0.82	1.132
oleate	1.007	1.466
phosphatidylcholine	0.91	0.753
acetate	0.096	0.775
glucAc	0.207	0.0
Rv0950ko	0.874	-0.172
Rv1096ko	0.214	0.066
Rv3684ko	0.049	0.0
delta_otsA_trehalose	0.871	-0.184