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 Rv3680/-:

update plot	correlation	link to info on gene
Rv3679/-	(cc=0.6755)	info on Rv3679/-
Rv0505c/serB1	(cc=0.6554)	info on Rv0505c/serB1
Rv1421/-	(cc=0.6354)	info on Rv1421/-
Rv2837c/-	(cc=0.6279)	info on Rv2837c/-
Rv3215/entC	(cc=0.5995)	info on Rv3215/entC
Rv0998/-	(cc=0.5957)	info on Rv0998/-
Rv2966c/-	(cc=0.5688)	info on Rv2966c/-
Rv1821/secA2	(cc=0.5413)	info on Rv1821/secA2
Rv2553c/-	(cc=0.5391)	info on Rv2553c/-
Rv1856c/-	(cc=0.524)	info on Rv1856c/-

Correlation of Rv3680/- with Rv1856c/-

Normalized LFCs for Rv3680/-:
(description and provenance of datasets)

	Rv3680/-	Rv1856c/-
Fe_supp_jason_reseq	1.689	1.959
low_pH_jason_reseq	1.673	-0.231
NO_jason_reseq	0.0	-0.362
B6_jason_reseq	0.0	0.14
MHCII_jason_reseq	0.0	0.437
Isoniazid02	-1.072	-2.325
Rifampicin4	-0.474	0.815
Ethambutol3	-0.59	-1.557
Meropenem3	-0.21	-0.607
Vancomycin16	-0.464	-1.035
Rv2680_day32	0.0	-0.48
H37Rv_KO_MarP	-0.766	1.236
hypoxia_3wks	-0.55	-2.117
hypoxia_6wks	-0.288	0.294
glycerol	2.455	3.31
cholesterol	1.612	3.37
AJ	0.0	-0.541
Bibs02	1.015	-0.273
Bibs02c	1.822	2.032
BL6	0.0	0.238
BL6a	1.812	1.502
BXD01	0.358	0.944
BXD010	0.128	0.0
BXD011	1.109	-0.54
BXD03	0.75	-0.315
BXD04	0.34	0.083
BXD05	0.369	0.256
BXD06	1.035	-0.097
BXD07	0.38	0.416
BXD08	0.253	-0.31
BXD09	0.69	0.095
CAST	0.0	-0.976
CCcont	1.765	2.111
DS01	0.83	0.31
DS02	0.217	1.99
DS04	1.301	2.135
DS0c	0.413	0.0
GP01	0.0	0.188
GP02	0.0	-0.194
GP0c	0.0	-0.551
NOD	0.0	-0.952
NZO	0.0	0.0
PWK	0.0	-0.635
H37Rv_KO_CtpC	0.162	2.266
H37Rv_KO_CtpD	0.445	0.566
H37Rv_KO_Rv1272	0.0	1.517
H37Rv_KO_SugABC	0.768	2.349
H37Rv_KO_MbtN	0.691	0.816
Trans05	0.0	-0.095
macrophage_unactivated	0.436	3.472
IL1	0.0	-1.032
Rapamycin	0.0	-0.328
Tcell	0.857	4.695
GMCSF	0.0	-1.281
IFNab	0.0	-0.323
IFNg	0.0	-1.296
IFNg_GMCSF1	0.0	-1.093
Rv1432_day32	0.0	-0.439
Rv1565c_day32	0.0	-0.182
secA2_input	-2.069	-0.266
delta_Rv3594	1.895	0.823
delta_Rv3717	3.237	1.248
delta_Rv3811	2.787	0.922
delta_Rv0954	0.375	-1.069
PonA1	1.599	-2.078
EccD1_KO	0.635	0.605
EspI_KO	0.878	0.148
PE35_KO	0.735	2.508
PPE68_KO	1.245	2.592
glycerol2	-0.193	0.394
lignocerate	-0.168	0.581
oleate	-0.196	4.392
phosphatidylcholine	-0.193	0.979
acetate	0.743	-0.173
glucAc	0.462	-0.07
Rv0950ko	-1.9	-2.545
Rv1096ko	-2.111	-3.049
Rv3684ko	-2.663	-2.512
delta_otsA_trehalose	0.895	0.367