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 Rv3485c/-

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

	Rv2300c/-	Rv3485c/-
Fe_supp_jason_reseq	-0.223	-0.297
low_pH_jason_reseq	-0.714	-1.303
NO_jason_reseq	0.071	-0.704
B6_jason_reseq	0.016	0.098
MHCII_jason_reseq	0.209	0.988
Isoniazid02	-0.113	0.819
Rifampicin4	-0.097	-0.774
Ethambutol3	-0.022	0.277
Meropenem3	-0.4	0.791
Vancomycin16	-0.194	0.061
Rv2680_day32	-1.068	-1.673
H37Rv_KO_MarP	-0.078	-0.082
hypoxia_3wks	0.171	0.415
hypoxia_6wks	0.177	-0.019
glycerol	-0.658	-0.278
cholesterol	-0.495	-0.524
AJ	-0.126	-0.37
Bibs02	-0.099	-0.298
Bibs02c	0.391	-0.094
BL6	0.237	-0.48
BL6a	0.194	-0.353
BXD01	0.109	-0.386
BXD010	0.549	-0.307
BXD011	0.467	-0.356
BXD03	0.122	-0.12
BXD04	0.014	-0.526
BXD05	-0.453	-0.611
BXD06	0.035	-0.288
BXD07	0.259	-0.359
BXD08	0.491	0.077
BXD09	0.253	-0.571
CAST	0.272	-0.269
CCcont	0.236	-1.139
DS01	0.062	-0.351
DS02	-0.076	-0.539
DS04	0.169	-0.632
DS0c	0.314	0.086
GP01	0.099	0.629
GP02	0.592	0.94
GP0c	-0.056	-0.038
NOD	0.234	-0.072
NZO	0.513	-0.4
PWK	0.428	-0.168
H37Rv_KO_CtpC	0.364	-0.241
H37Rv_KO_CtpD	0.696	0.161
H37Rv_KO_Rv1272	1.149	0.69
H37Rv_KO_SugABC	0.374	0.472
H37Rv_KO_MbtN	0.381	-0.488
Trans05	0.325	-0.112
macrophage_unactivated	0.139	-0.41
IL1	0.332	0.308
Rapamycin	0.04	-0.135
Tcell	0.029	-0.29
GMCSF	0.174	0.581
IFNab	0.121	0.145
IFNg	0.484	-0.088
IFNg_GMCSF1	0.531	0.035
Rv1432_day32	0.519	1.155
Rv1565c_day32	0.21	-1.016
secA2_input	0.913	0.612
delta_Rv3594	0.095	-0.548
delta_Rv3717	-0.249	-1.073
delta_Rv3811	-0.397	-0.512
delta_Rv0954	-0.649	-1.11
PonA1	-0.321	-0.941
EccD1_KO	0.227	-0.927
EspI_KO	0.465	-0.499
PE35_KO	0.376	-0.919
PPE68_KO	0.118	-0.464
glycerol2	0.738	0.205
lignocerate	0.82	-0.412
oleate	1.007	0.554
phosphatidylcholine	0.91	-0.081
acetate	0.096	-0.61
glucAc	0.207	-1.39
Rv0950ko	0.874	0.292
Rv1096ko	0.214	0.365
Rv3684ko	0.049	-1.104
delta_otsA_trehalose	0.871	-0.021