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 Rv0453/PPE11

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

	Rv2339/mmpL9	Rv0453/PPE11
Fe_supp_jason_reseq	0.283	0.316
low_pH_jason_reseq	-0.164	-1.062
NO_jason_reseq	-0.349	-0.339
B6_jason_reseq	-0.289	0.514
MHCII_jason_reseq	0.481	0.068
Isoniazid02	0.375	0.535
Rifampicin4	0.0	-0.119
Ethambutol3	0.568	0.539
Meropenem3	-0.052	0.121
Vancomycin16	0.146	0.0
Rv2680_day32	0.365	-0.072
H37Rv_KO_MarP	0.047	0.315
hypoxia_3wks	0.267	0.144
hypoxia_6wks	-0.177	-0.265
glycerol	-0.426	-0.607
cholesterol	-0.305	-0.039
AJ	0.247	-0.116
Bibs02	-0.127	0.087
Bibs02c	-0.276	0.294
BL6	0.196	-0.962
BL6a	0.211	0.136
BXD01	0.253	-0.407
BXD010	0.557	-0.788
BXD011	0.394	-0.361
BXD03	0.36	0.029
BXD04	0.565	-0.016
BXD05	0.615	-0.628
BXD06	0.413	-0.604
BXD07	0.295	-0.527
BXD08	0.087	-0.251
BXD09	0.41	-0.473
CAST	0.404	0.342
CCcont	-0.197	-1.136
DS01	0.154	0.313
DS02	-0.126	0.605
DS04	0.6	0.474
DS0c	0.578	0.167
GP01	0.591	-0.338
GP02	0.138	-0.053
GP0c	0.057	-0.953
NOD	1.289	-0.185
NZO	0.35	-0.314
PWK	0.47	0.222
H37Rv_KO_CtpC	0.488	-0.518
H37Rv_KO_CtpD	0.668	-0.069
H37Rv_KO_Rv1272	1.099	0.359
H37Rv_KO_SugABC	0.751	0.188
H37Rv_KO_MbtN	0.571	0.237
Trans05	1.072	0.372
macrophage_unactivated	0.42	0.338
IL1	0.611	1.106
Rapamycin	0.724	1.28
Tcell	-0.648	-3.421
GMCSF	1.225	1.708
IFNab	0.801	0.716
IFNg	1.056	1.799
IFNg_GMCSF1	0.55	1.31
Rv1432_day32	0.576	-0.185
Rv1565c_day32	0.3	-0.169
secA2_input	-0.631	-0.319
delta_Rv3594	-0.072	-0.15
delta_Rv3717	0.0	-0.458
delta_Rv3811	0.046	-0.574
delta_Rv0954	0.079	-0.707
PonA1	-0.293	-0.613
EccD1_KO	-0.046	-0.257
EspI_KO	-0.168	-0.722
PE35_KO	0.166	-0.688
PPE68_KO	0.355	-0.614
glycerol2	0.0	0.363
lignocerate	0.339	-0.062
oleate	0.081	0.635
phosphatidylcholine	0.231	0.38
acetate	-0.048	-0.527
glucAc	-0.227	-0.797
Rv0950ko	0.121	0.302
Rv1096ko	-1.095	-0.431
Rv3684ko	-0.223	0.259
delta_otsA_trehalose	-0.557	-0.974