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 Rv0053/rpsF:

update plot	correlation	link to info on gene
Rv3228/-	(cc=0.5477)	info on Rv3228/-
Rv3060c/-	(cc=0.5362)	info on Rv3060c/-
Rv2907c/rimM	(cc=0.5361)	info on Rv2907c/rimM
Rv3276c/purK	(cc=0.5335)	info on Rv3276c/purK
Rv0806c/cpsY	(cc=0.526)	info on Rv0806c/cpsY
Rv3032/-	(cc=0.5098)	info on Rv3032/-
Rv2971/-	(cc=0.5071)	info on Rv2971/-
Rv0348/-	(cc=0.4916)	info on Rv0348/-
Rv2913c/-	(cc=0.4889)	info on Rv2913c/-
Rv2042c/-	(cc=0.4828)	info on Rv2042c/-

Correlation of Rv0053/rpsF with Rv2971/-

Normalized LFCs for Rv0053/rpsF:
(description and provenance of datasets)

	Rv0053/rpsF	Rv2971/-
Fe_supp_jason_reseq	0.0	-0.684
low_pH_jason_reseq	0.0	-0.848
NO_jason_reseq	0.0	0.643
B6_jason_reseq	0.0	-0.189
MHCII_jason_reseq	0.0	-1.143
Isoniazid02	-1.379	0.0
Rifampicin4	-1.373	0.0
Ethambutol3	3.122	3.592
Meropenem3	1.198	0.266
Vancomycin16	0.883	0.305
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	0.793	0.892
hypoxia_3wks	0.0	-1.483
hypoxia_6wks	0.0	1.034
glycerol	0.0	-1.355
cholesterol	0.0	-0.972
AJ	0.0	-0.131
Bibs02	0.0	0.525
Bibs02c	0.0	-0.829
BL6	0.0	-0.225
BL6a	0.0	0.65
BXD01	0.0	0.136
BXD010	0.0	0.0
BXD011	0.0	0.734
BXD03	0.0	-0.649
BXD04	0.0	0.0
BXD05	0.0	0.329
BXD06	0.0	0.637
BXD07	0.0	0.612
BXD08	0.0	-0.639
BXD09	0.0	0.516
CAST	0.0	-0.913
CCcont	0.0	-0.369
DS01	0.0	1.287
DS02	0.0	0.881
DS04	0.194	1.238
DS0c	0.0	0.226
GP01	0.0	-0.662
GP02	0.0	-0.558
GP0c	0.0	-0.234
NOD	0.0	-0.404
NZO	0.0	-0.958
PWK	0.0	-0.627
H37Rv_KO_CtpC	0.0	-1.09
H37Rv_KO_CtpD	0.348	-0.723
H37Rv_KO_Rv1272	0.0	1.097
H37Rv_KO_SugABC	0.099	1.421
H37Rv_KO_MbtN	0.103	-0.119
Trans05	0.0	0.319
macrophage_unactivated	0.0	-0.628
IL1	0.0	0.519
Rapamycin	0.0	0.0
Tcell	0.0	-1.01
GMCSF	0.0	-0.671
IFNab	0.0	-0.768
IFNg	0.0	0.241
IFNg_GMCSF1	0.0	-1.354
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.122	0.82
delta_Rv3594	1.53	1.608
delta_Rv3717	1.513	0.979
delta_Rv3811	0.87	0.149
delta_Rv0954	1.852	0.129
PonA1	0.0	0.115
EccD1_KO	0.414	1.059
EspI_KO	1.791	1.668
PE35_KO	1.832	0.723
PPE68_KO	1.113	2.061
glycerol2	0.0	-0.311
lignocerate	0.0	-0.27
oleate	0.0	0.0
phosphatidylcholine	0.0	-0.487
acetate	0.0	0.166
glucAc	0.0	-0.501
Rv0950ko	0.0	1.517
Rv1096ko	0.0	2.636
Rv3684ko	1.444	1.359
delta_otsA_trehalose	0.254	0.0