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 Rv1088/PE9:

update plot	correlation	link to info on gene
Rv1918c/PPE35	(cc=0.6152)	info on Rv1918c/PPE35
Rv2548/vapC19	(cc=0.5699)	info on Rv2548/vapC19
Rv2717c/-	(cc=0.5658)	info on Rv2717c/-
Rv1059/-	(cc=0.5656)	info on Rv1059/-
Rv0799c/-	(cc=0.5429)	info on Rv0799c/-
Rv1521/fadD25	(cc=0.5388)	info on Rv1521/fadD25
Rv0260c/-	(cc=0.5319)	info on Rv0260c/-
Rv1502/-	(cc=0.5291)	info on Rv1502/-
Rv2835c/ugpA	(cc=0.5128)	info on Rv2835c/ugpA
Rv2809/-	(cc=0.5059)	info on Rv2809/-

Correlation of Rv1088/PE9 with Rv1918c/PPE35

Normalized LFCs for Rv1088/PE9:
(description and provenance of datasets)

	Rv1088/PE9	Rv1918c/PPE35
Fe_supp_jason_reseq	1.621	0.426
low_pH_jason_reseq	-2.414	-0.127
NO_jason_reseq	-0.108	-0.326
B6_jason_reseq	-0.142	-0.212
MHCII_jason_reseq	-1.374	-0.42
Isoniazid02	0.534	0.439
Rifampicin4	1.037	0.463
Ethambutol3	0.505	0.449
Meropenem3	1.364	0.129
Vancomycin16	0.268	0.18
Rv2680_day32	-3.328	-0.526
H37Rv_KO_MarP	-0.277	-0.339
hypoxia_3wks	0.299	0.06
hypoxia_6wks	0.021	-0.031
glycerol	-2.147	-0.671
cholesterol	-0.961	0.318
AJ	-0.827	0.432
Bibs02	0.842	0.189
Bibs02c	-0.981	0.083
BL6	0.674	0.442
BL6a	1.459	0.641
BXD01	1.37	0.383
BXD010	1.021	0.525
BXD011	1.285	0.747
BXD03	1.652	0.904
BXD04	0.061	0.687
BXD05	1.745	0.8
BXD06	1.016	0.584
BXD07	0.866	0.666
BXD08	1.823	0.605
BXD09	1.547	0.602
CAST	-0.445	0.21
CCcont	0.882	0.226
DS01	-1.567	0.185
DS02	0.21	0.17
DS04	-0.316	0.128
DS0c	-1.439	0.058
GP01	-1.37	0.102
GP02	-0.065	0.421
GP0c	0.253	0.658
NOD	-1.189	0.286
NZO	0.87	0.23
PWK	-1.445	0.153
H37Rv_KO_CtpC	0.971	0.711
H37Rv_KO_CtpD	0.683	1.161
H37Rv_KO_Rv1272	1.354	1.414
H37Rv_KO_SugABC	0.606	0.711
H37Rv_KO_MbtN	-0.659	1.033
Trans05	2.476	1.383
macrophage_unactivated	0.707	0.533
IL1	0.406	0.329
Rapamycin	0.663	0.411
Tcell	1.896	0.437
GMCSF	0.446	0.354
IFNab	0.106	0.151
IFNg	0.759	0.166
IFNg_GMCSF1	-0.569	0.738
Rv1432_day32	0.265	0.562
Rv1565c_day32	0.414	-0.227
secA2_input	-1.772	-0.441
delta_Rv3594	-0.278	-0.106
delta_Rv3717	0.54	-0.257
delta_Rv3811	0.776	0.366
delta_Rv0954	-0.631	0.014
PonA1	-0.248	-0.22
EccD1_KO	-0.707	-0.572
EspI_KO	0.0	-0.365
PE35_KO	-1.683	-0.44
PPE68_KO	-1.11	-0.518
glycerol2	0.266	-0.422
lignocerate	0.911	-0.242
oleate	-0.588	-0.041
phosphatidylcholine	0.585	-0.21
acetate	0.198	-0.47
glucAc	0.484	-0.123
Rv0950ko	-0.992	-0.488
Rv1096ko	-3.016	-1.001
Rv3684ko	-2.738	-0.347
delta_otsA_trehalose	0.539	-0.684