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 Rv0159c/PE3

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

	Rv2704/-	Rv0159c/PE3
Fe_supp_jason_reseq	-0.524	0.489
low_pH_jason_reseq	-1.223	-0.515
NO_jason_reseq	0.446	-0.165
B6_jason_reseq	0.083	0.378
MHCII_jason_reseq	0.254	0.273
Isoniazid02	-1.029	-1.23
Rifampicin4	0.449	0.138
Ethambutol3	-0.916	-0.674
Meropenem3	0.277	0.29
Vancomycin16	0.0	-0.523
Rv2680_day32	-0.596	0.421
H37Rv_KO_MarP	-0.439	0.096
hypoxia_3wks	0.195	-0.371
hypoxia_6wks	-0.616	-0.33
glycerol	0.151	-0.227
cholesterol	0.028	-0.35
AJ	-0.405	-0.403
Bibs02	0.16	0.185
Bibs02c	-0.291	0.006
BL6	0.321	0.374
BL6a	0.138	0.029
BXD01	-0.276	0.482
BXD010	0.537	0.334
BXD011	0.175	0.398
BXD03	0.16	0.232
BXD04	0.223	0.666
BXD05	0.547	0.303
BXD06	0.576	0.351
BXD07	0.11	0.234
BXD08	-0.318	0.473
BXD09	0.227	0.024
CAST	0.184	0.24
CCcont	-0.617	0.416
DS01	-0.176	-0.05
DS02	0.169	0.244
DS04	0.214	-0.309
DS0c	0.064	-0.354
GP01	0.087	0.707
GP02	0.714	0.599
GP0c	-0.067	0.089
NOD	0.508	0.539
NZO	-0.65	-0.121
PWK	0.279	0.045
H37Rv_KO_CtpC	-0.051	0.359
H37Rv_KO_CtpD	-0.442	0.905
H37Rv_KO_Rv1272	0.57	0.516
H37Rv_KO_SugABC	-0.426	0.492
H37Rv_KO_MbtN	0.21	0.06
Trans05	-0.687	0.465
macrophage_unactivated	0.287	0.821
IL1	0.727	2.287
Rapamycin	0.648	2.087
Tcell	0.251	-3.904
GMCSF	1.035	1.859
IFNab	0.868	1.868
IFNg	0.663	2.106
IFNg_GMCSF1	0.553	2.225
Rv1432_day32	-0.01	0.578
Rv1565c_day32	-0.166	-0.131
secA2_input	-0.069	0.085
delta_Rv3594	-0.219	-0.072
delta_Rv3717	-0.306	-0.165
delta_Rv3811	-0.601	0.043
delta_Rv0954	-0.705	0.195
PonA1	-0.605	-0.173
EccD1_KO	0.069	-0.428
EspI_KO	0.151	-0.419
PE35_KO	0.245	-0.551
PPE68_KO	-0.086	-0.65
glycerol2	-0.021	1.033
lignocerate	-0.347	0.894
oleate	0.21	0.749
phosphatidylcholine	-0.325	0.695
acetate	-0.025	0.12
glucAc	-1.153	-0.038
Rv0950ko	-0.145	0.485
Rv1096ko	-0.866	-0.507
Rv3684ko	-0.206	0.0
delta_otsA_trehalose	0.659	1.592