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 Rv0823c/-

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

	Rv1955/higB	Rv0823c/-
Fe_supp_jason_reseq	0.178	0.308
low_pH_jason_reseq	1.099	-1.039
NO_jason_reseq	0.213	0.701
B6_jason_reseq	0.985	0.626
MHCII_jason_reseq	-0.776	-0.773
Isoniazid02	0.135	-0.346
Rifampicin4	-0.577	-0.571
Ethambutol3	2.984	0.989
Meropenem3	-0.007	-0.128
Vancomycin16	-0.08	0.252
Rv2680_day32	0.567	-0.826
H37Rv_KO_MarP	-0.268	-0.172
hypoxia_3wks	-0.55	-0.65
hypoxia_6wks	0.775	-0.34
glycerol	-0.575	0.01
cholesterol	-0.782	0.067
AJ	0.027	0.166
Bibs02	0.503	0.122
Bibs02c	0.75	0.108
BL6	0.802	1.707
BL6a	1.218	1.049
BXD01	0.88	0.798
BXD010	0.917	0.914
BXD011	0.963	1.128
BXD03	0.321	0.95
BXD04	0.374	0.839
BXD05	0.854	1.499
BXD06	1.399	1.137
BXD07	1.252	1.336
BXD08	0.759	0.612
BXD09	1.111	1.18
CAST	0.414	1.004
CCcont	0.305	0.51
DS01	0.303	-0.077
DS02	0.455	-0.095
DS04	1.583	0.958
DS0c	-0.44	0.218
GP01	-0.179	0.988
GP02	1.142	0.51
GP0c	0.358	0.73
NOD	0.708	0.94
NZO	0.764	0.022
PWK	1.12	1.395
H37Rv_KO_CtpC	0.9	1.733
H37Rv_KO_CtpD	0.394	1.687
H37Rv_KO_Rv1272	1.515	0.897
H37Rv_KO_SugABC	-1.282	0.789
H37Rv_KO_MbtN	0.488	0.343
Trans05	1.807	1.739
macrophage_unactivated	1.493	-0.079
IL1	1.142	-0.4
Rapamycin	0.19	0.052
Tcell	0.678	-0.44
GMCSF	1.964	0.14
IFNab	0.683	0.475
IFNg	0.684	-0.588
IFNg_GMCSF1	0.984	-0.041
Rv1432_day32	-1.317	-1.978
Rv1565c_day32	-0.37	-0.545
secA2_input	0.421	-0.041
delta_Rv3594	0.234	-0.584
delta_Rv3717	0.33	-0.191
delta_Rv3811	0.321	-0.46
delta_Rv0954	0.464	-0.627
PonA1	-0.028	-0.514
EccD1_KO	-0.654	0.164
EspI_KO	0.519	0.131
PE35_KO	0.155	-0.283
PPE68_KO	0.403	-0.4
glycerol2	-0.579	-0.729
lignocerate	0.424	-0.205
oleate	-0.638	-0.179
phosphatidylcholine	-0.336	-0.326
acetate	-0.229	0.484
glucAc	-0.014	-0.304
Rv0950ko	-0.066	0.642
Rv1096ko	0.0	0.166
Rv3684ko	-1.136	0.033
delta_otsA_trehalose	-0.195	0.903