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 Rv2113/-:

update plot	correlation	link to info on gene
Rv0159c/PE3	(cc=0.856)	info on Rv0159c/PE3
Rv1817/-	(cc=0.8479)	info on Rv1817/-
Rv3815c/-	(cc=0.7418)	info on Rv3815c/-
Rv0453/PPE11	(cc=0.7248)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7197)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.6508)	info on Rv2822c/-
Rv3685c/cyp137	(cc=0.5386)	info on Rv3685c/cyp137
Rv3862c/whiB6	(cc=0.5193)	info on Rv3862c/whiB6
Rv1021/-	(cc=0.4871)	info on Rv1021/-
Rv2339/mmpL9	(cc=0.4851)	info on Rv2339/mmpL9

Correlation of Rv2113/- with Rv1817/-

Normalized LFCs for Rv2113/-:
(description and provenance of datasets)

	Rv2113/-	Rv1817/-
Fe_supp_jason_reseq	0.922	-0.223
low_pH_jason_reseq	-1.379	-0.388
NO_jason_reseq	-0.559	-0.714
B6_jason_reseq	-1.249	-0.232
MHCII_jason_reseq	-0.531	0.326
Isoniazid02	-1.043	0.215
Rifampicin4	0.406	0.0
Ethambutol3	0.657	0.612
Meropenem3	-0.462	0.316
Vancomycin16	-0.231	-0.04
Rv2680_day32	-0.825	-0.437
H37Rv_KO_MarP	0.159	-0.186
hypoxia_3wks	-0.012	0.116
hypoxia_6wks	-0.568	-0.203
glycerol	0.237	0.604
cholesterol	-0.405	0.241
AJ	0.356	-0.311
Bibs02	-0.372	0.738
Bibs02c	-0.209	0.358
BL6	0.418	-0.327
BL6a	0.169	-0.133
BXD01	-0.106	0.177
BXD010	-0.113	-0.209
BXD011	0.753	0.092
BXD03	0.123	-0.113
BXD04	-0.166	-0.103
BXD05	0.301	-0.219
BXD06	0.224	0.007
BXD07	0.171	-0.344
BXD08	0.265	0.091
BXD09	0.103	-0.331
CAST	-0.828	0.22
CCcont	0.169	-0.371
DS01	-0.335	0.453
DS02	0.098	0.334
DS04	-0.218	0.332
DS0c	0.11	0.409
GP01	0.072	-0.077
GP02	-0.087	0.301
GP0c	0.142	-0.088
NOD	-0.404	0.441
NZO	-0.604	0.069
PWK	-0.409	0.068
H37Rv_KO_CtpC	0.148	0.111
H37Rv_KO_CtpD	0.72	0.178
H37Rv_KO_Rv1272	0.551	1.0
H37Rv_KO_SugABC	1.132	-0.144
H37Rv_KO_MbtN	0.42	0.43
Trans05	0.939	1.011
macrophage_unactivated	1.143	1.588
IL1	2.886	2.201
Rapamycin	3.167	2.317
Tcell	-6.0	-4.923
GMCSF	2.756	2.26
IFNab	2.663	1.886
IFNg	2.905	2.397
IFNg_GMCSF1	2.963	2.385
Rv1432_day32	0.322	0.096
Rv1565c_day32	1.531	-0.156
secA2_input	0.128	-0.434
delta_Rv3594	-0.337	0.0
delta_Rv3717	-0.154	-0.028
delta_Rv3811	-0.312	0.28
delta_Rv0954	0.181	0.142
PonA1	-0.268	-0.059
EccD1_KO	0.148	0.687
EspI_KO	0.222	0.359
PE35_KO	-0.286	0.63
PPE68_KO	-0.147	0.56
glycerol2	0.894	0.085
lignocerate	0.616	-0.069
oleate	1.331	0.386
phosphatidylcholine	0.999	0.239
acetate	0.342	-0.156
glucAc	-0.082	-0.167
Rv0950ko	0.25	0.13
Rv1096ko	-0.13	-0.392
Rv3684ko	-0.233	-0.102
delta_otsA_trehalose	0.537	-0.085