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 Rv1955/higB:

update plot	correlation	link to info on gene
Rv1502/-	(cc=0.4896)	info on Rv1502/-
Rv1518/-	(cc=0.4595)	info on Rv1518/-
Rv0013/trpG	(cc=0.4585)	info on Rv0013/trpG
Rv1561/vapC11	(cc=0.4543)	info on Rv1561/vapC11
Rv2970A/-	(cc=0.4527)	info on Rv2970A/-
Rv0823c/-	(cc=0.4511)	info on Rv0823c/-
Rv2655c/-	(cc=0.4447)	info on Rv2655c/-
Rv0112/gca	(cc=0.4408)	info on Rv0112/gca
Rv0246/-	(cc=0.4364)	info on Rv0246/-
Rv1729c/-	(cc=0.4361)	info on Rv1729c/-

Correlation of Rv1955/higB with Rv0013/trpG

Normalized LFCs for Rv1955/higB:
(description and provenance of datasets)

	Rv1955/higB	Rv0013/trpG
Fe_supp_jason_reseq	0.178	0.766
low_pH_jason_reseq	1.099	2.652
NO_jason_reseq	0.213	1.273
B6_jason_reseq	0.985	0.0
MHCII_jason_reseq	-0.776	0.0
Isoniazid02	0.135	-0.221
Rifampicin4	-0.577	-1.681
Ethambutol3	2.984	4.238
Meropenem3	-0.007	-0.497
Vancomycin16	-0.08	-0.403
Rv2680_day32	0.567	-0.634
H37Rv_KO_MarP	-0.268	1.411
hypoxia_3wks	-0.55	-0.502
hypoxia_6wks	0.775	-0.263
glycerol	-0.575	0.0
cholesterol	-0.782	0.276
AJ	0.027	0.232
Bibs02	0.503	0.0
Bibs02c	0.75	0.0
BL6	0.802	0.238
BL6a	1.218	0.544
BXD01	0.88	0.358
BXD010	0.917	0.0
BXD011	0.963	0.0
BXD03	0.321	1.177
BXD04	0.374	0.124
BXD05	0.854	0.0
BXD06	1.399	0.566
BXD07	1.252	0.264
BXD08	0.759	0.467
BXD09	1.111	0.596
CAST	0.414	0.0
CCcont	0.305	1.002
DS01	0.303	0.236
DS02	0.455	0.414
DS04	1.583	0.0
DS0c	-0.44	0.0
GP01	-0.179	0.0
GP02	1.142	0.0
GP0c	0.358	0.551
NOD	0.708	0.0
NZO	0.764	0.0
PWK	1.12	0.196
H37Rv_KO_CtpC	0.9	0.0
H37Rv_KO_CtpD	0.394	0.348
H37Rv_KO_Rv1272	1.515	0.387
H37Rv_KO_SugABC	-1.282	0.0
H37Rv_KO_MbtN	0.488	0.0
Trans05	1.807	0.0
macrophage_unactivated	1.493	1.392
IL1	1.142	0.0
Rapamycin	0.19	-1.068
Tcell	0.678	0.0
GMCSF	1.964	0.739
IFNab	0.683	0.583
IFNg	0.684	-0.593
IFNg_GMCSF1	0.984	0.88
Rv1432_day32	-1.317	0.0
Rv1565c_day32	-0.37	-0.741
secA2_input	0.421	-1.061
delta_Rv3594	0.234	0.592
delta_Rv3717	0.33	-0.303
delta_Rv3811	0.321	-0.358
delta_Rv0954	0.464	-0.49
PonA1	-0.028	-0.437
EccD1_KO	-0.654	0.678
EspI_KO	0.519	1.104
PE35_KO	0.155	0.312
PPE68_KO	0.403	0.342
glycerol2	-0.579	0.13
lignocerate	0.424	0.967
oleate	-0.638	-0.634
phosphatidylcholine	-0.336	0.253
acetate	-0.229	0.69
glucAc	-0.014	0.501
Rv0950ko	-0.066	-1.33
Rv1096ko	0.0	-1.028
Rv3684ko	-1.136	-1.117
delta_otsA_trehalose	-0.195	-0.522