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 Rv0138/-:

update plot	correlation	link to info on gene
Rv3784/-	(cc=0.601)	info on Rv3784/-
Rv3440c/-	(cc=0.519)	info on Rv3440c/-
Rv0454/-	(cc=0.4943)	info on Rv0454/-
Rv3585/radA	(cc=0.4742)	info on Rv3585/radA
Rv3879c/espK	(cc=0.4715)	info on Rv3879c/espK
Rv3018c/PPE46	(cc=0.4683)	info on Rv3018c/PPE46
Rv1319c/-	(cc=0.4546)	info on Rv1319c/-
Rv1249c/-	(cc=0.4538)	info on Rv1249c/-
Rv3729/-	(cc=0.4481)	info on Rv3729/-
Rv3339c/icd1	(cc=0.4473)	info on Rv3339c/icd1

Correlation of Rv0138/- with Rv3585/radA

Normalized LFCs for Rv0138/-:
(description and provenance of datasets)

	Rv0138/-	Rv3585/radA
Fe_supp_jason_reseq	-0.759	-0.183
low_pH_jason_reseq	-0.778	-0.652
NO_jason_reseq	-0.131	-0.037
B6_jason_reseq	-0.133	-0.008
MHCII_jason_reseq	-0.222	0.374
Isoniazid02	1.099	0.471
Rifampicin4	-0.398	-0.165
Ethambutol3	2.393	1.833
Meropenem3	0.652	1.053
Vancomycin16	-0.096	-0.111
Rv2680_day32	1.396	0.097
H37Rv_KO_MarP	0.306	-0.017
hypoxia_3wks	0.187	-0.1
hypoxia_6wks	0.236	-0.457
glycerol	0.767	0.452
cholesterol	0.272	0.301
AJ	0.635	0.326
Bibs02	0.045	-0.009
Bibs02c	0.499	-0.118
BL6	-0.08	-0.333
BL6a	0.346	-0.23
BXD01	0.259	-0.181
BXD010	-0.77	0.087
BXD011	0.054	-0.323
BXD03	0.329	0.19
BXD04	-0.094	-0.527
BXD05	0.052	-0.257
BXD06	-0.024	-0.041
BXD07	0.196	-0.007
BXD08	-0.231	-0.162
BXD09	-0.547	-0.124
CAST	0.627	-0.035
CCcont	0.037	-0.932
DS01	-0.139	-0.342
DS02	-0.274	0.199
DS04	0.364	-0.247
DS0c	0.009	0.127
GP01	-0.302	0.305
GP02	0.915	0.068
GP0c	0.219	0.54
NOD	-0.116	0.495
NZO	0.386	0.236
PWK	0.22	0.517
H37Rv_KO_CtpC	0.305	-0.041
H37Rv_KO_CtpD	1.534	0.483
H37Rv_KO_Rv1272	0.13	0.055
H37Rv_KO_SugABC	0.987	0.675
H37Rv_KO_MbtN	0.582	-0.026
Trans05	0.136	0.547
macrophage_unactivated	0.846	0.401
IL1	-0.442	-0.469
Rapamycin	0.322	0.295
Tcell	-0.44	0.212
GMCSF	-0.143	0.734
IFNab	-0.759	0.52
IFNg	0.043	0.021
IFNg_GMCSF1	0.459	0.255
Rv1432_day32	0.67	0.373
Rv1565c_day32	-0.924	-0.171
secA2_input	-0.348	1.208
delta_Rv3594	-0.791	-0.558
delta_Rv3717	-0.395	-0.415
delta_Rv3811	-0.714	-0.595
delta_Rv0954	-1.23	-0.612
PonA1	-0.491	-0.361
EccD1_KO	0.089	-0.053
EspI_KO	-0.391	0.151
PE35_KO	0.07	0.274
PPE68_KO	-0.243	0.016
glycerol2	0.647	0.263
lignocerate	0.549	-0.066
oleate	0.275	0.771
phosphatidylcholine	0.37	0.42
acetate	0.291	0.043
glucAc	0.318	-0.668
Rv0950ko	-0.039	0.76
Rv1096ko	-0.196	0.516
Rv3684ko	0.17	1.074
delta_otsA_trehalose	-0.057	0.142