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 Rv1410c/-

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

	Rv1254/-	Rv1410c/-
Fe_supp_jason_reseq	0.0	3.44
low_pH_jason_reseq	0.0	1.673
NO_jason_reseq	0.0	-0.735
B6_jason_reseq	0.0	1.287
MHCII_jason_reseq	0.135	0.543
Isoniazid02	-0.183	1.099
Rifampicin4	-0.341	-6.0
Ethambutol3	-0.32	0.253
Meropenem3	-0.151	-2.427
Vancomycin16	-0.334	-6.0
Rv2680_day32	0.0	-0.459
H37Rv_KO_MarP	-0.684	-4.874
hypoxia_3wks	0.0	0.387
hypoxia_6wks	0.0	0.958
glycerol	0.202	0.979
cholesterol	0.398	-0.208
AJ	0.0	-0.262
Bibs02	0.0	0.23
Bibs02c	0.574	0.214
BL6	0.0	0.727
BL6a	0.0	0.712
BXD01	0.0	0.516
BXD010	0.0	-0.034
BXD011	0.0	0.721
BXD03	0.0	0.632
BXD04	0.0	0.0
BXD05	0.0	0.719
BXD06	0.0	1.166
BXD07	0.0	0.498
BXD08	0.0	0.317
BXD09	0.0	0.795
CAST	0.0	-0.632
CCcont	0.0	3.121
DS01	0.236	-0.488
DS02	0.217	-0.922
DS04	0.533	0.15
DS0c	0.0	-0.671
GP01	0.0	0.559
GP02	0.0	0.992
GP0c	0.0	2.603
NOD	0.0	-0.254
NZO	0.0	-0.225
PWK	0.0	-1.474
H37Rv_KO_CtpC	0.0	-0.233
H37Rv_KO_CtpD	0.0	-0.221
H37Rv_KO_Rv1272	0.0	0.479
H37Rv_KO_SugABC	0.0	0.73
H37Rv_KO_MbtN	0.0	1.573
Trans05	0.0	1.08
macrophage_unactivated	0.0	0.691
IL1	0.0	-1.154
Rapamycin	0.0	-0.163
Tcell	0.0	-0.74
GMCSF	0.0	-0.288
IFNab	0.0	1.847
IFNg	0.0	-0.607
IFNg_GMCSF1	0.0	-0.167
Rv1432_day32	0.0	-0.683
Rv1565c_day32	0.218	0.886
secA2_input	-0.412	1.158
delta_Rv3594	-1.427	-6.0
delta_Rv3717	1.258	-5.682
delta_Rv3811	-0.454	-6.0
delta_Rv0954	-1.206	-6.0
PonA1	-1.235	-6.0
EccD1_KO	0.0	-3.039
EspI_KO	0.0	-3.032
PE35_KO	0.767	-2.719
PPE68_KO	0.442	-2.198
glycerol2	0.0	-0.059
lignocerate	0.0	0.19
oleate	0.0	-0.248
phosphatidylcholine	0.0	-0.181
acetate	0.0	-0.07
glucAc	0.0	0.236
Rv0950ko	0.0	-0.697
Rv1096ko	0.0	-2.009
Rv3684ko	0.0	-0.567
delta_otsA_trehalose	0.133	-1.379