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 Rv1871c/-

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

	Rv2339/mmpL9	Rv1871c/-
Fe_supp_jason_reseq	0.283	-0.912
low_pH_jason_reseq	-0.164	-0.53
NO_jason_reseq	-0.349	0.473
B6_jason_reseq	-0.289	-1.258
MHCII_jason_reseq	0.481	-1.425
Isoniazid02	0.375	1.439
Rifampicin4	0.0	0.479
Ethambutol3	0.568	0.428
Meropenem3	-0.052	0.461
Vancomycin16	0.146	0.456
Rv2680_day32	0.365	-0.682
H37Rv_KO_MarP	0.047	-0.285
hypoxia_3wks	0.267	0.75
hypoxia_6wks	-0.177	0.073
glycerol	-0.426	-0.992
cholesterol	-0.305	-0.324
AJ	0.247	-0.239
Bibs02	-0.127	-0.36
Bibs02c	-0.276	-1.199
BL6	0.196	-0.055
BL6a	0.211	-0.277
BXD01	0.253	-0.095
BXD010	0.557	0.395
BXD011	0.394	0.603
BXD03	0.36	-0.029
BXD04	0.565	-0.269
BXD05	0.615	0.71
BXD06	0.413	0.057
BXD07	0.295	0.007
BXD08	0.087	0.157
BXD09	0.41	-0.145
CAST	0.404	0.37
CCcont	-0.197	-0.471
DS01	0.154	-0.039
DS02	-0.126	-0.501
DS04	0.6	-0.177
DS0c	0.578	-0.277
GP01	0.591	1.05
GP02	0.138	0.11
GP0c	0.057	0.703
NOD	1.289	0.485
NZO	0.35	-0.688
PWK	0.47	-0.604
H37Rv_KO_CtpC	0.488	0.112
H37Rv_KO_CtpD	0.668	0.495
H37Rv_KO_Rv1272	1.099	0.893
H37Rv_KO_SugABC	0.751	0.349
H37Rv_KO_MbtN	0.571	1.584
Trans05	1.072	0.698
macrophage_unactivated	0.42	0.625
IL1	0.611	-0.403
Rapamycin	0.724	0.476
Tcell	-0.648	-0.345
GMCSF	1.225	0.869
IFNab	0.801	0.686
IFNg	1.056	-0.168
IFNg_GMCSF1	0.55	0.292
Rv1432_day32	0.576	-0.485
Rv1565c_day32	0.3	-0.009
secA2_input	-0.631	-0.994
delta_Rv3594	-0.072	-1.137
delta_Rv3717	0.0	-1.158
delta_Rv3811	0.046	-0.758
delta_Rv0954	0.079	-0.908
PonA1	-0.293	-1.138
EccD1_KO	-0.046	-0.306
EspI_KO	-0.168	0.915
PE35_KO	0.166	-0.184
PPE68_KO	0.355	-0.074
glycerol2	0.0	0.265
lignocerate	0.339	-0.578
oleate	0.081	0.698
phosphatidylcholine	0.231	0.37
acetate	-0.048	-0.836
glucAc	-0.227	-1.325
Rv0950ko	0.121	-0.874
Rv1096ko	-1.095	-1.378
Rv3684ko	-0.223	-0.707
delta_otsA_trehalose	-0.557	0.11