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 Rv3815c/-

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

	Rv2113/-	Rv3815c/-
Fe_supp_jason_reseq	0.922	0.979
low_pH_jason_reseq	-1.379	-0.796
NO_jason_reseq	-0.559	-0.126
B6_jason_reseq	-1.249	0.078
MHCII_jason_reseq	-0.531	0.437
Isoniazid02	-1.043	1.352
Rifampicin4	0.406	-0.631
Ethambutol3	0.657	1.757
Meropenem3	-0.462	0.574
Vancomycin16	-0.231	-1.353
Rv2680_day32	-0.825	-2.585
H37Rv_KO_MarP	0.159	0.539
hypoxia_3wks	-0.012	-0.303
hypoxia_6wks	-0.568	-0.956
glycerol	0.237	0.942
cholesterol	-0.405	0.987
AJ	0.356	0.247
Bibs02	-0.372	-0.274
Bibs02c	-0.209	0.488
BL6	0.418	0.605
BL6a	0.169	0.432
BXD01	-0.106	0.552
BXD010	-0.113	-0.555
BXD011	0.753	1.267
BXD03	0.123	-0.091
BXD04	-0.166	0.913
BXD05	0.301	-0.439
BXD06	0.224	-0.064
BXD07	0.171	-0.093
BXD08	0.265	0.31
BXD09	0.103	0.161
CAST	-0.828	0.205
CCcont	0.169	0.808
DS01	-0.335	0.0
DS02	0.098	-1.134
DS04	-0.218	0.364
DS0c	0.11	-0.471
GP01	0.072	0.678
GP02	-0.087	0.633
GP0c	0.142	0.369
NOD	-0.404	0.386
NZO	-0.604	-0.257
PWK	-0.409	0.413
H37Rv_KO_CtpC	0.148	-0.126
H37Rv_KO_CtpD	0.72	1.339
H37Rv_KO_Rv1272	0.551	1.376
H37Rv_KO_SugABC	1.132	-0.298
H37Rv_KO_MbtN	0.42	0.907
Trans05	0.939	0.61
macrophage_unactivated	1.143	1.079
IL1	2.886	2.231
Rapamycin	3.167	2.397
Tcell	-6.0	-5.116
GMCSF	2.756	2.883
IFNab	2.663	2.352
IFNg	2.905	2.05
IFNg_GMCSF1	2.963	1.709
Rv1432_day32	0.322	0.15
Rv1565c_day32	1.531	0.084
secA2_input	0.128	-0.485
delta_Rv3594	-0.337	0.327
delta_Rv3717	-0.154	1.309
delta_Rv3811	-0.312	1.083
delta_Rv0954	0.181	0.976
PonA1	-0.268	0.616
EccD1_KO	0.148	0.918
EspI_KO	0.222	0.473
PE35_KO	-0.286	-0.403
PPE68_KO	-0.147	0.48
glycerol2	0.894	0.893
lignocerate	0.616	0.992
oleate	1.331	0.379
phosphatidylcholine	0.999	0.769
acetate	0.342	1.43
glucAc	-0.082	1.041
Rv0950ko	0.25	-0.498
Rv1096ko	-0.13	-0.115
Rv3684ko	-0.233	0.465
delta_otsA_trehalose	0.537	-1.184