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 Rv0017c/rodA

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

	Rv1254/-	Rv0017c/rodA
Fe_supp_jason_reseq	0.0	2.392
low_pH_jason_reseq	0.0	2.923
NO_jason_reseq	0.0	-0.281
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.135	0.503
Isoniazid02	-0.183	-1.005
Rifampicin4	-0.341	-2.32
Ethambutol3	-0.32	-2.802
Meropenem3	-0.151	-1.846
Vancomycin16	-0.334	-4.6
Rv2680_day32	0.0	1.168
H37Rv_KO_MarP	-0.684	-4.322
hypoxia_3wks	0.0	0.447
hypoxia_6wks	0.0	0.656
glycerol	0.202	1.891
cholesterol	0.398	1.357
AJ	0.0	-0.866
Bibs02	0.0	1.507
Bibs02c	0.574	0.488
BL6	0.0	0.805
BL6a	0.0	0.769
BXD01	0.0	1.247
BXD010	0.0	-0.141
BXD011	0.0	0.54
BXD03	0.0	0.424
BXD04	0.0	0.236
BXD05	0.0	0.903
BXD06	0.0	0.254
BXD07	0.0	0.323
BXD08	0.0	0.653
BXD09	0.0	0.14
CAST	0.0	-0.39
CCcont	0.0	2.042
DS01	0.236	0.83
DS02	0.217	-0.117
DS04	0.533	0.822
DS0c	0.0	0.217
GP01	0.0	1.006
GP02	0.0	-0.194
GP0c	0.0	1.008
NOD	0.0	-0.524
NZO	0.0	-1.246
PWK	0.0	-1.225
H37Rv_KO_CtpC	0.0	0.571
H37Rv_KO_CtpD	0.0	1.363
H37Rv_KO_Rv1272	0.0	0.824
H37Rv_KO_SugABC	0.0	0.453
H37Rv_KO_MbtN	0.0	0.943
Trans05	0.0	0.642
macrophage_unactivated	0.0	0.385
IL1	0.0	-0.679
Rapamycin	0.0	-1.363
Tcell	0.0	0.398
GMCSF	0.0	-1.658
IFNab	0.0	-0.13
IFNg	0.0	-1.344
IFNg_GMCSF1	0.0	0.258
Rv1432_day32	0.0	2.066
Rv1565c_day32	0.218	0.0
secA2_input	-0.412	-2.537
delta_Rv3594	-1.427	0.737
delta_Rv3717	1.258	0.369
delta_Rv3811	-0.454	1.068
delta_Rv0954	-1.206	-2.989
PonA1	-1.235	-2.28
EccD1_KO	0.0	-0.921
EspI_KO	0.0	-0.847
PE35_KO	0.767	0.505
PPE68_KO	0.442	0.349
glycerol2	0.0	-3.464
lignocerate	0.0	-1.587
oleate	0.0	-3.311
phosphatidylcholine	0.0	-1.737
acetate	0.0	-0.504
glucAc	0.0	-0.083
Rv0950ko	0.0	-1.716
Rv1096ko	0.0	-1.007
Rv3684ko	0.0	0.488
delta_otsA_trehalose	0.133	1.148