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 Rv3060c/-

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

	Rv0053/rpsF	Rv3060c/-
Fe_supp_jason_reseq	0.0	-0.284
low_pH_jason_reseq	0.0	-0.56
NO_jason_reseq	0.0	-0.21
B6_jason_reseq	0.0	-0.168
MHCII_jason_reseq	0.0	0.013
Isoniazid02	-1.379	-0.314
Rifampicin4	-1.373	-0.393
Ethambutol3	3.122	2.165
Meropenem3	1.198	0.212
Vancomycin16	0.883	-0.17
Rv2680_day32	0.0	-0.044
H37Rv_KO_MarP	0.793	0.813
hypoxia_3wks	0.0	-0.431
hypoxia_6wks	0.0	-0.643
glycerol	0.0	-1.012
cholesterol	0.0	-0.686
AJ	0.0	-0.04
Bibs02	0.0	-0.632
Bibs02c	0.0	0.036
BL6	0.0	-1.318
BL6a	0.0	-0.75
BXD01	0.0	-0.981
BXD010	0.0	-1.011
BXD011	0.0	-0.872
BXD03	0.0	-0.581
BXD04	0.0	-1.323
BXD05	0.0	-0.371
BXD06	0.0	-0.814
BXD07	0.0	-0.964
BXD08	0.0	-0.63
BXD09	0.0	-1.128
CAST	0.0	-0.327
CCcont	0.0	-0.957
DS01	0.0	-0.53
DS02	0.0	-0.972
DS04	0.194	-0.655
DS0c	0.0	-0.647
GP01	0.0	-1.267
GP02	0.0	0.01
GP0c	0.0	-1.594
NOD	0.0	-0.688
NZO	0.0	0.208
PWK	0.0	-0.331
H37Rv_KO_CtpC	0.0	-0.106
H37Rv_KO_CtpD	0.348	0.222
H37Rv_KO_Rv1272	0.0	-1.167
H37Rv_KO_SugABC	0.099	-0.678
H37Rv_KO_MbtN	0.103	-0.978
Trans05	0.0	-0.441
macrophage_unactivated	0.0	-0.893
IL1	0.0	-1.112
Rapamycin	0.0	-0.393
Tcell	0.0	-0.505
GMCSF	0.0	0.063
IFNab	0.0	-0.508
IFNg	0.0	-0.27
IFNg_GMCSF1	0.0	-0.487
Rv1432_day32	0.0	0.098
Rv1565c_day32	0.0	-0.586
secA2_input	-0.122	-0.554
delta_Rv3594	1.53	0.064
delta_Rv3717	1.513	0.22
delta_Rv3811	0.87	-0.32
delta_Rv0954	1.852	0.176
PonA1	0.0	0.484
EccD1_KO	0.414	0.414
EspI_KO	1.791	0.388
PE35_KO	1.832	0.461
PPE68_KO	1.113	-0.397
glycerol2	0.0	0.353
lignocerate	0.0	-0.371
oleate	0.0	-0.398
phosphatidylcholine	0.0	0.183
acetate	0.0	-0.785
glucAc	0.0	-0.589
Rv0950ko	0.0	0.0
Rv1096ko	0.0	-0.371
Rv3684ko	1.444	-0.675
delta_otsA_trehalose	0.254	0.494