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 Rv2339/mmpL9:

update plot	correlation	link to info on gene
Rv1984c/cfp21	(cc=0.6427)	info on Rv1984c/cfp21
Rv1918c/PPE35	(cc=0.5915)	info on Rv1918c/PPE35
Rv3862c/whiB6	(cc=0.5504)	info on Rv3862c/whiB6
Rv1521/fadD25	(cc=0.5484)	info on Rv1521/fadD25
Rv1817/-	(cc=0.5212)	info on Rv1817/-
Rv1548c/PPE21	(cc=0.5209)	info on Rv1548c/PPE21
Rv3164c/moxR3	(cc=0.5205)	info on Rv3164c/moxR3
Rv1917c/PPE34	(cc=0.5069)	info on Rv1917c/PPE34
Rv0453/PPE11	(cc=0.5034)	info on Rv0453/PPE11
Rv1871c/-	(cc=0.5003)	info on Rv1871c/-

Correlation of Rv2339/mmpL9 with Rv1817/-

Normalized LFCs for Rv2339/mmpL9:
(description and provenance of datasets)

	Rv2339/mmpL9	Rv1817/-
Fe_supp_jason_reseq	0.283	-0.223
low_pH_jason_reseq	-0.164	-0.388
NO_jason_reseq	-0.349	-0.714
B6_jason_reseq	-0.289	-0.232
MHCII_jason_reseq	0.481	0.326
Isoniazid02	0.375	0.215
Rifampicin4	0.0	0.0
Ethambutol3	0.568	0.612
Meropenem3	-0.052	0.316
Vancomycin16	0.146	-0.04
Rv2680_day32	0.365	-0.437
H37Rv_KO_MarP	0.047	-0.186
hypoxia_3wks	0.267	0.116
hypoxia_6wks	-0.177	-0.203
glycerol	-0.426	0.604
cholesterol	-0.305	0.241
AJ	0.247	-0.311
Bibs02	-0.127	0.738
Bibs02c	-0.276	0.358
BL6	0.196	-0.327
BL6a	0.211	-0.133
BXD01	0.253	0.177
BXD010	0.557	-0.209
BXD011	0.394	0.092
BXD03	0.36	-0.113
BXD04	0.565	-0.103
BXD05	0.615	-0.219
BXD06	0.413	0.007
BXD07	0.295	-0.344
BXD08	0.087	0.091
BXD09	0.41	-0.331
CAST	0.404	0.22
CCcont	-0.197	-0.371
DS01	0.154	0.453
DS02	-0.126	0.334
DS04	0.6	0.332
DS0c	0.578	0.409
GP01	0.591	-0.077
GP02	0.138	0.301
GP0c	0.057	-0.088
NOD	1.289	0.441
NZO	0.35	0.069
PWK	0.47	0.068
H37Rv_KO_CtpC	0.488	0.111
H37Rv_KO_CtpD	0.668	0.178
H37Rv_KO_Rv1272	1.099	1.0
H37Rv_KO_SugABC	0.751	-0.144
H37Rv_KO_MbtN	0.571	0.43
Trans05	1.072	1.011
macrophage_unactivated	0.42	1.588
IL1	0.611	2.201
Rapamycin	0.724	2.317
Tcell	-0.648	-4.923
GMCSF	1.225	2.26
IFNab	0.801	1.886
IFNg	1.056	2.397
IFNg_GMCSF1	0.55	2.385
Rv1432_day32	0.576	0.096
Rv1565c_day32	0.3	-0.156
secA2_input	-0.631	-0.434
delta_Rv3594	-0.072	0.0
delta_Rv3717	0.0	-0.028
delta_Rv3811	0.046	0.28
delta_Rv0954	0.079	0.142
PonA1	-0.293	-0.059
EccD1_KO	-0.046	0.687
EspI_KO	-0.168	0.359
PE35_KO	0.166	0.63
PPE68_KO	0.355	0.56
glycerol2	0.0	0.085
lignocerate	0.339	-0.069
oleate	0.081	0.386
phosphatidylcholine	0.231	0.239
acetate	-0.048	-0.156
glucAc	-0.227	-0.167
Rv0950ko	0.121	0.13
Rv1096ko	-1.095	-0.392
Rv3684ko	-0.223	-0.102
delta_otsA_trehalose	-0.557	-0.085