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 Rv0505c/serB1

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

	Rv3680/-	Rv0505c/serB1
Fe_supp_jason_reseq	1.689	0.527
low_pH_jason_reseq	1.673	1.081
NO_jason_reseq	0.0	-0.344
B6_jason_reseq	0.0	-1.334
MHCII_jason_reseq	0.0	-0.512
Isoniazid02	-1.072	0.0
Rifampicin4	-0.474	0.498
Ethambutol3	-0.59	0.078
Meropenem3	-0.21	0.535
Vancomycin16	-0.464	-0.178
Rv2680_day32	0.0	-0.33
H37Rv_KO_MarP	-0.766	-0.54
hypoxia_3wks	-0.55	0.913
hypoxia_6wks	-0.288	0.892
glycerol	2.455	1.631
cholesterol	1.612	0.0
AJ	0.0	-0.212
Bibs02	1.015	0.152
Bibs02c	1.822	0.629
BL6	0.0	0.731
BL6a	1.812	1.347
BXD01	0.358	0.944
BXD010	0.128	2.061
BXD011	1.109	1.306
BXD03	0.75	1.146
BXD04	0.34	0.949
BXD05	0.369	1.335
BXD06	1.035	1.57
BXD07	0.38	0.942
BXD08	0.253	1.956
BXD09	0.69	1.244
CAST	0.0	0.0
CCcont	1.765	1.992
DS01	0.83	0.197
DS02	0.217	0.0
DS04	1.301	0.583
DS0c	0.413	0.181
GP01	0.0	0.082
GP02	0.0	0.4
GP0c	0.0	0.391
NOD	0.0	-0.205
NZO	0.0	-0.38
PWK	0.0	-0.374
H37Rv_KO_CtpC	0.162	0.488
H37Rv_KO_CtpD	0.445	0.862
H37Rv_KO_Rv1272	0.0	1.248
H37Rv_KO_SugABC	0.768	2.417
H37Rv_KO_MbtN	0.691	0.791
Trans05	0.0	0.554
macrophage_unactivated	0.436	-0.581
IL1	0.0	0.329
Rapamycin	0.0	-0.565
Tcell	0.857	0.362
GMCSF	0.0	-0.85
IFNab	0.0	-1.197
IFNg	0.0	-1.267
IFNg_GMCSF1	0.0	-0.792
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-2.069	-1.983
delta_Rv3594	1.895	1.869
delta_Rv3717	3.237	1.343
delta_Rv3811	2.787	1.862
delta_Rv0954	0.375	1.154
PonA1	1.599	0.898
EccD1_KO	0.635	-0.263
EspI_KO	0.878	0.0
PE35_KO	0.735	0.916
PPE68_KO	1.245	0.694
glycerol2	-0.193	-0.775
lignocerate	-0.168	-0.794
oleate	-0.196	0.22
phosphatidylcholine	-0.193	-0.406
acetate	0.743	-0.352
glucAc	0.462	0.19
Rv0950ko	-1.9	-0.754
Rv1096ko	-2.111	-2.289
Rv3684ko	-2.663	-1.968
delta_otsA_trehalose	0.895	0.084