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 Rv2345/-

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

	Rv2300c/-	Rv2345/-
Fe_supp_jason_reseq	-0.223	-0.019
low_pH_jason_reseq	-0.714	-0.962
NO_jason_reseq	0.071	-0.053
B6_jason_reseq	0.016	-0.063
MHCII_jason_reseq	0.209	0.065
Isoniazid02	-0.113	-1.199
Rifampicin4	-0.097	0.509
Ethambutol3	-0.022	-1.019
Meropenem3	-0.4	-1.409
Vancomycin16	-0.194	-0.655
Rv2680_day32	-1.068	-0.466
H37Rv_KO_MarP	-0.078	-0.02
hypoxia_3wks	0.171	0.032
hypoxia_6wks	0.177	0.257
glycerol	-0.658	0.192
cholesterol	-0.495	-0.086
AJ	-0.126	0.0
Bibs02	-0.099	-0.278
Bibs02c	0.391	-0.205
BL6	0.237	0.138
BL6a	0.194	0.118
BXD01	0.109	0.14
BXD010	0.549	0.141
BXD011	0.467	-0.262
BXD03	0.122	-0.04
BXD04	0.014	0.291
BXD05	-0.453	0.374
BXD06	0.035	0.147
BXD07	0.259	0.238
BXD08	0.491	0.434
BXD09	0.253	0.199
CAST	0.272	-0.225
CCcont	0.236	0.024
DS01	0.062	0.0
DS02	-0.076	-0.498
DS04	0.169	-0.142
DS0c	0.314	-0.057
GP01	0.099	0.277
GP02	0.592	0.072
GP0c	-0.056	0.147
NOD	0.234	0.265
NZO	0.513	-0.237
PWK	0.428	-0.058
H37Rv_KO_CtpC	0.364	0.373
H37Rv_KO_CtpD	0.696	0.605
H37Rv_KO_Rv1272	1.149	0.291
H37Rv_KO_SugABC	0.374	0.767
H37Rv_KO_MbtN	0.381	0.628
Trans05	0.325	0.501
macrophage_unactivated	0.139	-0.114
IL1	0.332	0.338
Rapamycin	0.04	0.473
Tcell	0.029	0.039
GMCSF	0.174	0.599
IFNab	0.121	0.311
IFNg	0.484	0.216
IFNg_GMCSF1	0.531	0.182
Rv1432_day32	0.519	0.194
Rv1565c_day32	0.21	0.175
secA2_input	0.913	0.233
delta_Rv3594	0.095	0.271
delta_Rv3717	-0.249	0.055
delta_Rv3811	-0.397	0.352
delta_Rv0954	-0.649	0.371
PonA1	-0.321	-0.321
EccD1_KO	0.227	0.704
EspI_KO	0.465	0.767
PE35_KO	0.376	0.429
PPE68_KO	0.118	0.176
glycerol2	0.738	0.277
lignocerate	0.82	0.284
oleate	1.007	0.702
phosphatidylcholine	0.91	0.153
acetate	0.096	-0.462
glucAc	0.207	-0.232
Rv0950ko	0.874	0.434
Rv1096ko	0.214	-0.567
Rv3684ko	0.049	-0.54
delta_otsA_trehalose	0.871	0.582