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 Rv2704/-:

update plot	correlation	link to info on gene
Rv1947/-	(cc=0.539)	info on Rv1947/-
Rv2389c/rpfD	(cc=0.4731)	info on Rv2389c/rpfD
Rv1770/-	(cc=0.4697)	info on Rv1770/-
Rv1000c/-	(cc=0.4429)	info on Rv1000c/-
Rv2067c/-	(cc=0.439)	info on Rv2067c/-
Rv2658c/-	(cc=0.4381)	info on Rv2658c/-
Rv0868c/moaD2	(cc=0.4188)	info on Rv0868c/moaD2
Rv3840/-	(cc=0.4148)	info on Rv3840/-
Rv0159c/PE3	(cc=0.4089)	info on Rv0159c/PE3
Rv2976c/ung	(cc=0.4081)	info on Rv2976c/ung

Correlation of Rv2704/- with Rv0868c/moaD2

Normalized LFCs for Rv2704/-:
(description and provenance of datasets)

	Rv2704/-	Rv0868c/moaD2
Fe_supp_jason_reseq	-0.524	-0.182
low_pH_jason_reseq	-1.223	-1.238
NO_jason_reseq	0.446	0.186
B6_jason_reseq	0.083	-0.452
MHCII_jason_reseq	0.254	-0.221
Isoniazid02	-1.029	-2.314
Rifampicin4	0.449	0.65
Ethambutol3	-0.916	-1.626
Meropenem3	0.277	-0.904
Vancomycin16	0.0	0.082
Rv2680_day32	-0.596	0.668
H37Rv_KO_MarP	-0.439	-0.494
hypoxia_3wks	0.195	0.925
hypoxia_6wks	-0.616	1.437
glycerol	0.151	0.825
cholesterol	0.028	1.62
AJ	-0.405	0.627
Bibs02	0.16	0.086
Bibs02c	-0.291	0.099
BL6	0.321	1.182
BL6a	0.138	0.535
BXD01	-0.276	0.519
BXD010	0.537	0.906
BXD011	0.175	0.615
BXD03	0.16	0.957
BXD04	0.223	0.982
BXD05	0.547	0.523
BXD06	0.576	1.048
BXD07	0.11	0.374
BXD08	-0.318	0.647
BXD09	0.227	0.528
CAST	0.184	-0.983
CCcont	-0.617	0.27
DS01	-0.176	-0.139
DS02	0.169	0.315
DS04	0.214	0.086
DS0c	0.064	1.01
GP01	0.087	-0.928
GP02	0.714	1.009
GP0c	-0.067	0.02
NOD	0.508	-0.737
NZO	-0.65	0.396
PWK	0.279	0.475
H37Rv_KO_CtpC	-0.051	-0.268
H37Rv_KO_CtpD	-0.442	-0.39
H37Rv_KO_Rv1272	0.57	0.145
H37Rv_KO_SugABC	-0.426	-0.405
H37Rv_KO_MbtN	0.21	-0.104
Trans05	-0.687	-0.052
macrophage_unactivated	0.287	-0.174
IL1	0.727	0.828
Rapamycin	0.648	0.555
Tcell	0.251	1.153
GMCSF	1.035	0.618
IFNab	0.868	0.308
IFNg	0.663	1.149
IFNg_GMCSF1	0.553	0.782
Rv1432_day32	-0.01	0.528
Rv1565c_day32	-0.166	-1.891
secA2_input	-0.069	-0.366
delta_Rv3594	-0.219	-0.142
delta_Rv3717	-0.306	-0.93
delta_Rv3811	-0.601	-0.607
delta_Rv0954	-0.705	-0.695
PonA1	-0.605	0.012
EccD1_KO	0.069	-0.539
EspI_KO	0.151	-0.511
PE35_KO	0.245	-0.785
PPE68_KO	-0.086	-0.912
glycerol2	-0.021	0.873
lignocerate	-0.347	0.472
oleate	0.21	1.341
phosphatidylcholine	-0.325	0.804
acetate	-0.025	-0.168
glucAc	-1.153	-0.12
Rv0950ko	-0.145	-1.134
Rv1096ko	-0.866	-1.146
Rv3684ko	-0.206	-1.389
delta_otsA_trehalose	0.659	-0.631