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 Rv3105c/prfB:

update plot	correlation	link to info on gene
Rv1616/-	(cc=0.5046)	info on Rv1616/-
Rv2492/-	(cc=0.4924)	info on Rv2492/-
Rv1083/-	(cc=0.4849)	info on Rv1083/-
Rv0149/-	(cc=0.4731)	info on Rv0149/-
Rv2275/-	(cc=0.4661)	info on Rv2275/-
Rv3796/-	(cc=0.4625)	info on Rv3796/-
Rv3278c/-	(cc=0.4563)	info on Rv3278c/-
Rv1215c/-	(cc=0.4555)	info on Rv1215c/-
Rv0728c/serA2	(cc=0.448)	info on Rv0728c/serA2
Rv3429/PPE59	(cc=0.4476)	info on Rv3429/PPE59

Correlation of Rv3105c/prfB with Rv3796/-

Normalized LFCs for Rv3105c/prfB:
(description and provenance of datasets)

	Rv3105c/prfB	Rv3796/-
Fe_supp_jason_reseq	1.76	0.216
low_pH_jason_reseq	-0.211	-0.253
NO_jason_reseq	0.583	-0.063
B6_jason_reseq	-0.292	-0.018
MHCII_jason_reseq	0.0	-0.072
Isoniazid02	0.135	-0.361
Rifampicin4	0.49	0.623
Ethambutol3	0.22	-0.165
Meropenem3	2.735	0.966
Vancomycin16	0.48	0.085
Rv2680_day32	-0.131	-0.562
H37Rv_KO_MarP	0.226	0.477
hypoxia_3wks	1.252	0.0
hypoxia_6wks	0.0	-0.198
glycerol	-0.202	-0.48
cholesterol	0.0	-0.036
AJ	2.086	1.324
Bibs02	0.0	-0.091
Bibs02c	-0.209	0.897
BL6	2.658	0.714
BL6a	1.131	1.187
BXD01	1.222	0.694
BXD010	1.387	0.944
BXD011	0.923	0.969
BXD03	1.893	0.803
BXD04	0.896	0.849
BXD05	0.0	1.394
BXD06	1.252	0.664
BXD07	0.712	0.75
BXD08	1.686	0.98
BXD09	1.018	0.971
CAST	0.746	0.552
CCcont	0.852	0.396
DS01	0.0	0.392
DS02	-0.217	0.361
DS04	0.0	0.564
DS0c	0.379	0.811
GP01	0.847	1.283
GP02	0.0	0.027
GP0c	-0.13	0.613
NOD	0.0	1.059
NZO	2.021	1.195
PWK	1.009	0.594
H37Rv_KO_CtpC	0.284	0.521
H37Rv_KO_CtpD	0.0	0.584
H37Rv_KO_Rv1272	3.081	1.414
H37Rv_KO_SugABC	0.321	0.936
H37Rv_KO_MbtN	0.884	0.828
Trans05	0.119	0.764
macrophage_unactivated	0.947	0.527
IL1	-0.341	0.024
Rapamycin	0.328	0.295
Tcell	-0.186	0.124
GMCSF	-0.636	-0.04
IFNab	0.163	-0.045
IFNg	0.422	-0.104
IFNg_GMCSF1	-0.556	0.189
Rv1432_day32	0.0	-0.269
Rv1565c_day32	0.0	0.374
secA2_input	-0.412	0.302
delta_Rv3594	-1.62	0.211
delta_Rv3717	0.205	0.356
delta_Rv3811	-1.761	0.104
delta_Rv0954	0.0	0.746
PonA1	-0.743	0.28
EccD1_KO	0.793	-0.335
EspI_KO	2.561	-0.73
PE35_KO	0.0	-0.298
PPE68_KO	0.0	-0.352
glycerol2	0.332	0.235
lignocerate	-0.826	0.078
oleate	1.207	0.586
phosphatidylcholine	0.27	0.246
acetate	0.321	-0.229
glucAc	-1.868	-0.347
Rv0950ko	-0.395	0.057
Rv1096ko	-0.832	-0.115
Rv3684ko	-1.428	0.239
delta_otsA_trehalose	-0.675	-0.027