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 Rv1999c/-:

update plot	correlation	link to info on gene
Rv0089/-	(cc=0.721)	info on Rv0089/-
Rv2499c/-	(cc=0.6894)	info on Rv2499c/-
Rv2007c/fdxA	(cc=0.6802)	info on Rv2007c/fdxA
Rv3354/-	(cc=0.6696)	info on Rv3354/-
Rv2076c/-	(cc=0.6597)	info on Rv2076c/-
Rv2633c/-	(cc=0.651)	info on Rv2633c/-
Rv2028c/-	(cc=0.645)	info on Rv2028c/-
Rv3059/cyp136	(cc=0.6442)	info on Rv3059/cyp136
Rv1846c/blaI	(cc=0.6335)	info on Rv1846c/blaI
Rv1974/-	(cc=0.6314)	info on Rv1974/-

Correlation of Rv1999c/- with Rv0089/-

Normalized LFCs for Rv1999c/-:
(description and provenance of datasets)

	Rv1999c/-	Rv0089/-
Fe_supp_jason_reseq	0.032	-0.617
low_pH_jason_reseq	-0.609	-0.221
NO_jason_reseq	0.239	0.047
B6_jason_reseq	-0.061	0.241
MHCII_jason_reseq	0.316	0.487
Isoniazid02	0.188	0.877
Rifampicin4	0.628	-0.701
Ethambutol3	0.17	-0.483
Meropenem3	-0.29	-0.564
Vancomycin16	0.032	0.0
Rv2680_day32	0.398	1.554
H37Rv_KO_MarP	-0.042	1.943
hypoxia_3wks	-0.227	-0.59
hypoxia_6wks	-0.397	-0.699
glycerol	-0.499	-1.188
cholesterol	-0.351	-0.61
AJ	-0.097	0.069
Bibs02	0.007	0.098
Bibs02c	-0.088	0.0
BL6	-0.925	-1.724
BL6a	-0.676	-1.411
BXD01	-0.679	-1.681
BXD010	-0.928	-1.478
BXD011	-0.795	-1.727
BXD03	-0.578	-1.397
BXD04	-0.7	-0.973
BXD05	-1.079	-1.529
BXD06	-0.89	-1.642
BXD07	-0.664	-2.006
BXD08	-0.867	-2.382
BXD09	-0.907	-1.596
CAST	-0.35	0.492
CCcont	-0.974	-0.977
DS01	0.053	-0.209
DS02	0.118	0.153
DS04	0.333	0.462
DS0c	-0.515	0.308
GP01	0.218	0.326
GP02	-0.615	-1.336
GP0c	-0.365	-0.489
NOD	-0.202	0.145
NZO	-0.228	-0.1
PWK	-0.359	0.389
H37Rv_KO_CtpC	-1.177	-1.138
H37Rv_KO_CtpD	-0.724	-3.064
H37Rv_KO_Rv1272	-0.021	-0.742
H37Rv_KO_SugABC	-0.338	-0.481
H37Rv_KO_MbtN	-0.29	-1.571
Trans05	-0.035	0.008
macrophage_unactivated	-0.038	-2.727
IL1	-0.522	-1.246
Rapamycin	-0.623	-2.071
Tcell	-0.238	-1.3
GMCSF	0.356	-1.848
IFNab	-0.78	-2.524
IFNg	-0.505	-1.871
IFNg_GMCSF1	0.072	-0.936
Rv1432_day32	0.248	0.301
Rv1565c_day32	0.122	0.594
secA2_input	-0.374	-1.028
delta_Rv3594	-0.021	0.0
delta_Rv3717	0.216	-0.216
delta_Rv3811	0.326	0.755
delta_Rv0954	-0.335	0.442
PonA1	-0.308	-0.308
EccD1_KO	0.296	-0.118
EspI_KO	-0.088	1.221
PE35_KO	0.63	0.204
PPE68_KO	0.31	1.497
glycerol2	0.765	1.494
lignocerate	0.848	1.736
oleate	0.119	-0.505
phosphatidylcholine	0.899	1.304
acetate	0.648	2.168
glucAc	0.925	1.508
Rv0950ko	0.199	-0.169
Rv1096ko	-0.13	0.983
Rv3684ko	0.445	1.019
delta_otsA_trehalose	0.475	1.304