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 Rv1521/fadD25

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

	Rv2339/mmpL9	Rv1521/fadD25
Fe_supp_jason_reseq	0.283	1.408
low_pH_jason_reseq	-0.164	-0.495
NO_jason_reseq	-0.349	0.0
B6_jason_reseq	-0.289	0.444
MHCII_jason_reseq	0.481	0.125
Isoniazid02	0.375	-0.183
Rifampicin4	0.0	0.133
Ethambutol3	0.568	0.322
Meropenem3	-0.052	0.081
Vancomycin16	0.146	0.379
Rv2680_day32	0.365	0.161
H37Rv_KO_MarP	0.047	0.0
hypoxia_3wks	0.267	0.698
hypoxia_6wks	-0.177	0.576
glycerol	-0.426	-0.404
cholesterol	-0.305	-0.35
AJ	0.247	0.274
Bibs02	-0.127	0.539
Bibs02c	-0.276	-0.537
BL6	0.196	0.492
BL6a	0.211	0.408
BXD01	0.253	0.906
BXD010	0.557	1.149
BXD011	0.394	0.802
BXD03	0.36	1.018
BXD04	0.565	1.19
BXD05	0.615	0.952
BXD06	0.413	0.737
BXD07	0.295	0.688
BXD08	0.087	1.121
BXD09	0.41	0.668
CAST	0.404	0.052
CCcont	-0.197	0.478
DS01	0.154	0.027
DS02	-0.126	0.0
DS04	0.6	-0.045
DS0c	0.578	-0.05
GP01	0.591	0.634
GP02	0.138	1.092
GP0c	0.057	0.726
NOD	1.289	0.524
NZO	0.35	-0.023
PWK	0.47	-0.59
H37Rv_KO_CtpC	0.488	1.032
H37Rv_KO_CtpD	0.668	1.28
H37Rv_KO_Rv1272	1.099	1.45
H37Rv_KO_SugABC	0.751	0.767
H37Rv_KO_MbtN	0.571	1.982
Trans05	1.072	1.332
macrophage_unactivated	0.42	0.505
IL1	0.611	0.552
Rapamycin	0.724	0.703
Tcell	-0.648	0.404
GMCSF	1.225	0.129
IFNab	0.801	0.72
IFNg	1.056	0.476
IFNg_GMCSF1	0.55	0.531
Rv1432_day32	0.576	0.169
Rv1565c_day32	0.3	0.313
secA2_input	-0.631	-0.762
delta_Rv3594	-0.072	0.515
delta_Rv3717	0.0	-0.225
delta_Rv3811	0.046	0.0
delta_Rv0954	0.079	-0.127
PonA1	-0.293	-0.18
EccD1_KO	-0.046	0.033
EspI_KO	-0.168	0.314
PE35_KO	0.166	0.347
PPE68_KO	0.355	0.65
glycerol2	0.0	-0.149
lignocerate	0.339	-0.496
oleate	0.081	0.067
phosphatidylcholine	0.231	-0.045
acetate	-0.048	-0.308
glucAc	-0.227	-0.773
Rv0950ko	0.121	0.193
Rv1096ko	-1.095	-1.194
Rv3684ko	-0.223	-0.793
delta_otsA_trehalose	-0.557	0.144