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 Rv1141c/echA11

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

	Rv2300c/-	Rv1141c/echA11
Fe_supp_jason_reseq	-0.223	-1.143
low_pH_jason_reseq	-0.714	-1.589
NO_jason_reseq	0.071	0.365
B6_jason_reseq	0.016	-0.567
MHCII_jason_reseq	0.209	-0.357
Isoniazid02	-0.113	-0.201
Rifampicin4	-0.097	0.872
Ethambutol3	-0.022	-0.078
Meropenem3	-0.4	0.399
Vancomycin16	-0.194	-0.151
Rv2680_day32	-1.068	-0.615
H37Rv_KO_MarP	-0.078	0.072
hypoxia_3wks	0.171	-0.148
hypoxia_6wks	0.177	0.104
glycerol	-0.658	0.478
cholesterol	-0.495	-0.485
AJ	-0.126	0.121
Bibs02	-0.099	-0.152
Bibs02c	0.391	1.144
BL6	0.237	0.694
BL6a	0.194	1.115
BXD01	0.109	0.577
BXD010	0.549	0.13
BXD011	0.467	2.406
BXD03	0.122	0.515
BXD04	0.014	0.477
BXD05	-0.453	-0.083
BXD06	0.035	0.221
BXD07	0.259	0.805
BXD08	0.491	0.228
BXD09	0.253	0.496
CAST	0.272	0.582
CCcont	0.236	0.401
DS01	0.062	-0.031
DS02	-0.076	-0.244
DS04	0.169	0.013
DS0c	0.314	0.057
GP01	0.099	1.232
GP02	0.592	0.471
GP0c	-0.056	0.902
NOD	0.234	0.496
NZO	0.513	-0.361
PWK	0.428	0.423
H37Rv_KO_CtpC	0.364	0.81
H37Rv_KO_CtpD	0.696	1.174
H37Rv_KO_Rv1272	1.149	0.686
H37Rv_KO_SugABC	0.374	1.109
H37Rv_KO_MbtN	0.381	0.806
Trans05	0.325	0.467
macrophage_unactivated	0.139	0.363
IL1	0.332	0.163
Rapamycin	0.04	0.129
Tcell	0.029	0.837
GMCSF	0.174	0.977
IFNab	0.121	0.021
IFNg	0.484	-0.115
IFNg_GMCSF1	0.531	0.955
Rv1432_day32	0.519	-0.292
Rv1565c_day32	0.21	0.325
secA2_input	0.913	-0.063
delta_Rv3594	0.095	0.285
delta_Rv3717	-0.249	0.159
delta_Rv3811	-0.397	0.7
delta_Rv0954	-0.649	0.424
PonA1	-0.321	-0.504
EccD1_KO	0.227	1.5
EspI_KO	0.465	1.483
PE35_KO	0.376	0.718
PPE68_KO	0.118	1.488
glycerol2	0.738	0.921
lignocerate	0.82	1.108
oleate	1.007	1.231
phosphatidylcholine	0.91	1.325
acetate	0.096	0.545
glucAc	0.207	0.461
Rv0950ko	0.874	-0.353
Rv1096ko	0.214	0.103
Rv3684ko	0.049	-0.508
delta_otsA_trehalose	0.871	1.225