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 Rv3840/-

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

	Rv2704/-	Rv3840/-
Fe_supp_jason_reseq	-0.524	-0.158
low_pH_jason_reseq	-1.223	-1.121
NO_jason_reseq	0.446	0.129
B6_jason_reseq	0.083	-0.108
MHCII_jason_reseq	0.254	-0.192
Isoniazid02	-1.029	-0.764
Rifampicin4	0.449	-0.374
Ethambutol3	-0.916	-0.652
Meropenem3	0.277	0.43
Vancomycin16	0.0	-0.584
Rv2680_day32	-0.596	0.162
H37Rv_KO_MarP	-0.439	0.182
hypoxia_3wks	0.195	0.191
hypoxia_6wks	-0.616	0.311
glycerol	0.151	-0.032
cholesterol	0.028	0.119
AJ	-0.405	0.21
Bibs02	0.16	0.123
Bibs02c	-0.291	-0.69
BL6	0.321	0.27
BL6a	0.138	-0.059
BXD01	-0.276	0.375
BXD010	0.537	0.567
BXD011	0.175	0.188
BXD03	0.16	0.728
BXD04	0.223	0.453
BXD05	0.547	0.83
BXD06	0.576	0.55
BXD07	0.11	0.367
BXD08	-0.318	0.353
BXD09	0.227	0.68
CAST	0.184	0.402
CCcont	-0.617	-0.058
DS01	-0.176	0.05
DS02	0.169	0.537
DS04	0.214	0.233
DS0c	0.064	0.167
GP01	0.087	0.636
GP02	0.714	1.625
GP0c	-0.067	0.811
NOD	0.508	0.439
NZO	-0.65	-0.095
PWK	0.279	0.323
H37Rv_KO_CtpC	-0.051	0.238
H37Rv_KO_CtpD	-0.442	0.113
H37Rv_KO_Rv1272	0.57	0.542
H37Rv_KO_SugABC	-0.426	0.935
H37Rv_KO_MbtN	0.21	0.526
Trans05	-0.687	-0.102
macrophage_unactivated	0.287	-0.076
IL1	0.727	-0.208
Rapamycin	0.648	0.47
Tcell	0.251	0.166
GMCSF	1.035	0.111
IFNab	0.868	0.49
IFNg	0.663	0.2
IFNg_GMCSF1	0.553	0.101
Rv1432_day32	-0.01	0.349
Rv1565c_day32	-0.166	0.039
secA2_input	-0.069	0.377
delta_Rv3594	-0.219	-0.415
delta_Rv3717	-0.306	0.074
delta_Rv3811	-0.601	-0.164
delta_Rv0954	-0.705	-0.225
PonA1	-0.605	-0.421
EccD1_KO	0.069	-0.431
EspI_KO	0.151	-0.191
PE35_KO	0.245	-0.537
PPE68_KO	-0.086	-0.576
glycerol2	-0.021	0.314
lignocerate	-0.347	-0.073
oleate	0.21	0.625
phosphatidylcholine	-0.325	0.108
acetate	-0.025	-0.487
glucAc	-1.153	-0.564
Rv0950ko	-0.145	0.697
Rv1096ko	-0.866	0.0
Rv3684ko	-0.206	0.049
delta_otsA_trehalose	0.659	-1.073