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 Rv1502/-

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

	Rv1955/higB	Rv1502/-
Fe_supp_jason_reseq	0.178	1.364
low_pH_jason_reseq	1.099	-0.403
NO_jason_reseq	0.213	0.457
B6_jason_reseq	0.985	-0.589
MHCII_jason_reseq	-0.776	-0.627
Isoniazid02	0.135	0.78
Rifampicin4	-0.577	-0.065
Ethambutol3	2.984	0.527
Meropenem3	-0.007	-0.214
Vancomycin16	-0.08	-0.334
Rv2680_day32	0.567	-0.632
H37Rv_KO_MarP	-0.268	-0.825
hypoxia_3wks	-0.55	0.14
hypoxia_6wks	0.775	1.247
glycerol	-0.575	-0.897
cholesterol	-0.782	-0.475
AJ	0.027	-0.096
Bibs02	0.503	0.0
Bibs02c	0.75	0.829
BL6	0.802	1.837
BL6a	1.218	2.05
BXD01	0.88	0.586
BXD010	0.917	1.119
BXD011	0.963	1.807
BXD03	0.321	2.184
BXD04	0.374	1.576
BXD05	0.854	1.881
BXD06	1.399	1.55
BXD07	1.252	1.608
BXD08	0.759	1.016
BXD09	1.111	1.791
CAST	0.414	-0.095
CCcont	0.305	1.478
DS01	0.303	-0.197
DS02	0.455	-0.279
DS04	1.583	-0.533
DS0c	-0.44	-0.379
GP01	-0.179	-0.715
GP02	1.142	-0.672
GP0c	0.358	-0.427
NOD	0.708	-0.093
NZO	0.764	-0.082
PWK	1.12	1.032
H37Rv_KO_CtpC	0.9	1.177
H37Rv_KO_CtpD	0.394	2.462
H37Rv_KO_Rv1272	1.515	1.763
H37Rv_KO_SugABC	-1.282	0.446
H37Rv_KO_MbtN	0.488	1.472
Trans05	1.807	2.472
macrophage_unactivated	1.493	0.0
IL1	1.142	-0.107
Rapamycin	0.19	0.107
Tcell	0.678	0.055
GMCSF	1.964	0.182
IFNab	0.683	0.0
IFNg	0.684	0.804
IFNg_GMCSF1	0.984	0.371
Rv1432_day32	-1.317	-3.119
Rv1565c_day32	-0.37	0.599
secA2_input	0.421	0.063
delta_Rv3594	0.234	0.6
delta_Rv3717	0.33	0.619
delta_Rv3811	0.321	0.825
delta_Rv0954	0.464	0.636
PonA1	-0.028	0.53
EccD1_KO	-0.654	0.365
EspI_KO	0.519	0.0
PE35_KO	0.155	-0.537
PPE68_KO	0.403	-0.093
glycerol2	-0.579	-1.156
lignocerate	0.424	-0.179
oleate	-0.638	-2.215
phosphatidylcholine	-0.336	-0.885
acetate	-0.229	-0.078
glucAc	-0.014	0.159
Rv0950ko	-0.066	-0.522
Rv1096ko	0.0	-1.592
Rv3684ko	-1.136	-0.481
delta_otsA_trehalose	-0.195	-0.525