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 Rv2067c/-

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

	Rv2704/-	Rv2067c/-
Fe_supp_jason_reseq	-0.524	0.284
low_pH_jason_reseq	-1.223	-0.075
NO_jason_reseq	0.446	0.572
B6_jason_reseq	0.083	0.049
MHCII_jason_reseq	0.254	0.0
Isoniazid02	-1.029	0.0
Rifampicin4	0.449	0.393
Ethambutol3	-0.916	0.084
Meropenem3	0.277	0.818
Vancomycin16	0.0	0.159
Rv2680_day32	-0.596	0.383
H37Rv_KO_MarP	-0.439	-0.138
hypoxia_3wks	0.195	-0.327
hypoxia_6wks	-0.616	0.033
glycerol	0.151	0.05
cholesterol	0.028	-0.112
AJ	-0.405	0.61
Bibs02	0.16	0.713
Bibs02c	-0.291	0.403
BL6	0.321	0.843
BL6a	0.138	0.936
BXD01	-0.276	0.153
BXD010	0.537	0.919
BXD011	0.175	0.54
BXD03	0.16	0.66
BXD04	0.223	0.66
BXD05	0.547	0.646
BXD06	0.576	0.703
BXD07	0.11	0.337
BXD08	-0.318	0.324
BXD09	0.227	0.572
CAST	0.184	0.444
CCcont	-0.617	0.67
DS01	-0.176	0.142
DS02	0.169	0.35
DS04	0.214	-0.024
DS0c	0.064	0.303
GP01	0.087	0.426
GP02	0.714	1.662
GP0c	-0.067	0.078
NOD	0.508	0.633
NZO	-0.65	0.12
PWK	0.279	-0.099
H37Rv_KO_CtpC	-0.051	0.06
H37Rv_KO_CtpD	-0.442	-0.132
H37Rv_KO_Rv1272	0.57	1.155
H37Rv_KO_SugABC	-0.426	0.241
H37Rv_KO_MbtN	0.21	1.744
Trans05	-0.687	0.995
macrophage_unactivated	0.287	0.941
IL1	0.727	0.483
Rapamycin	0.648	0.534
Tcell	0.251	0.453
GMCSF	1.035	0.552
IFNab	0.868	0.345
IFNg	0.663	0.465
IFNg_GMCSF1	0.553	0.584
Rv1432_day32	-0.01	0.43
Rv1565c_day32	-0.166	0.415
secA2_input	-0.069	-0.538
delta_Rv3594	-0.219	0.017
delta_Rv3717	-0.306	-0.176
delta_Rv3811	-0.601	0.033
delta_Rv0954	-0.705	-0.295
PonA1	-0.605	-0.278
EccD1_KO	0.069	-0.536
EspI_KO	0.151	-0.103
PE35_KO	0.245	0.458
PPE68_KO	-0.086	0.074
glycerol2	-0.021	0.333
lignocerate	-0.347	0.666
oleate	0.21	0.247
phosphatidylcholine	-0.325	0.887
acetate	-0.025	0.667
glucAc	-1.153	0.246
Rv0950ko	-0.145	-0.154
Rv1096ko	-0.866	-0.941
Rv3684ko	-0.206	-0.236
delta_otsA_trehalose	0.659	0.61