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 Rv1254/-:

update plot	correlation	link to info on gene
Rv2195/qcrA	(cc=0.5168)	info on Rv2195/qcrA
Rv2004c/-	(cc=0.4678)	info on Rv2004c/-
Rv0479c/-	(cc=0.4554)	info on Rv0479c/-
Rv2176/pknL	(cc=0.4476)	info on Rv2176/pknL
Rv0016c/pbpA	(cc=0.4144)	info on Rv0016c/pbpA
Rv0260c/-	(cc=0.3995)	info on Rv0260c/-
Rv3593/lpqF	(cc=0.3839)	info on Rv3593/lpqF
Rv0017c/rodA	(cc=0.3792)	info on Rv0017c/rodA
Rv0589/mce2A	(cc=0.3791)	info on Rv0589/mce2A
Rv1410c/-	(cc=0.3763)	info on Rv1410c/-

Correlation of Rv1254/- with Rv2195/qcrA

Normalized LFCs for Rv1254/-:
(description and provenance of datasets)

	Rv1254/-	Rv2195/qcrA
Fe_supp_jason_reseq	0.0	0.0
low_pH_jason_reseq	0.0	0.979
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.135	0.0
Isoniazid02	-0.183	-0.383
Rifampicin4	-0.341	0.0
Ethambutol3	-0.32	-0.153
Meropenem3	-0.151	-0.151
Vancomycin16	-0.334	-0.334
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.684	0.195
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.202	0.0
cholesterol	0.398	0.0
AJ	0.0	0.0
Bibs02	0.0	0.642
Bibs02c	0.574	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.0	0.0
DS01	0.236	0.0
DS02	0.217	0.0
DS04	0.533	0.682
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.162
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	0.283
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.218	0.0
secA2_input	-0.412	0.47
delta_Rv3594	-1.427	-1.898
delta_Rv3717	1.258	-1.258
delta_Rv3811	-0.454	-1.487
delta_Rv0954	-1.206	-1.782
PonA1	-1.235	-1.592
EccD1_KO	0.0	0.0
EspI_KO	0.0	0.0
PE35_KO	0.767	0.403
PPE68_KO	0.442	0.442
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.143
Rv0950ko	0.0	0.347
Rv1096ko	0.0	-0.793
Rv3684ko	0.0	-0.861
delta_otsA_trehalose	0.133	0.133