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 Rv0853c/pdc:

update plot	correlation	link to info on gene
Rv1074c/fadA3	(cc=0.5105)	info on Rv1074c/fadA3
Rv0923c/-	(cc=0.4748)	info on Rv0923c/-
Rv1168c/PPE17	(cc=0.4311)	info on Rv1168c/PPE17
Rv3079c/-	(cc=0.4291)	info on Rv3079c/-
Rv3238c/-	(cc=0.4244)	info on Rv3238c/-
Rv1739c/-	(cc=0.3809)	info on Rv1739c/-
Rv2453c/mobA	(cc=0.3794)	info on Rv2453c/mobA
Rv2951c/-	(cc=0.3771)	info on Rv2951c/-
Rv0098/fcoT	(cc=0.3648)	info on Rv0098/fcoT
Rv3120/-	(cc=0.3587)	info on Rv3120/-

Correlation of Rv0853c/pdc with Rv0923c/-

Normalized LFCs for Rv0853c/pdc:
(description and provenance of datasets)

	Rv0853c/pdc	Rv0923c/-
Fe_supp_jason_reseq	-0.346	-0.59
low_pH_jason_reseq	-0.278	0.37
NO_jason_reseq	-1.189	-0.635
B6_jason_reseq	0.341	-0.28
MHCII_jason_reseq	0.358	-0.508
Isoniazid02	0.137	0.055
Rifampicin4	0.255	0.333
Ethambutol3	0.663	0.524
Meropenem3	0.089	0.562
Vancomycin16	0.141	0.135
Rv2680_day32	-0.592	0.36
H37Rv_KO_MarP	-0.135	0.141
hypoxia_3wks	-0.407	0.0
hypoxia_6wks	0.238	-0.111
glycerol	-0.35	-0.408
cholesterol	-0.408	0.18
AJ	-0.632	0.365
Bibs02	-0.196	0.332
Bibs02c	-0.797	-0.279
BL6	-0.283	0.295
BL6a	-0.088	0.099
BXD01	0.064	0.743
BXD010	0.35	0.431
BXD011	0.197	0.27
BXD03	-0.04	0.526
BXD04	0.222	0.566
BXD05	0.33	0.796
BXD06	0.304	0.443
BXD07	0.161	0.473
BXD08	0.039	0.646
BXD09	-0.196	0.561
CAST	-0.878	0.227
CCcont	-0.032	0.519
DS01	0.366	0.585
DS02	0.581	0.369
DS04	0.594	1.179
DS0c	-0.08	0.844
GP01	-1.223	-0.605
GP02	-0.166	0.9
GP0c	-0.442	-0.449
NOD	1.1	0.973
NZO	-0.328	0.459
PWK	-0.117	0.0
H37Rv_KO_CtpC	-0.035	-0.3
H37Rv_KO_CtpD	0.421	0.009
H37Rv_KO_Rv1272	0.164	-0.503
H37Rv_KO_SugABC	0.225	0.425
H37Rv_KO_MbtN	0.386	-0.128
Trans05	0.863	-0.163
macrophage_unactivated	0.903	1.433
IL1	0.543	0.572
Rapamycin	0.384	1.068
Tcell	-0.029	0.733
GMCSF	0.261	1.288
IFNab	0.245	0.822
IFNg	0.147	0.537
IFNg_GMCSF1	1.178	1.449
Rv1432_day32	0.287	0.948
Rv1565c_day32	0.077	-0.158
secA2_input	-0.363	0.384
delta_Rv3594	0.54	0.594
delta_Rv3717	-0.083	0.074
delta_Rv3811	0.4	-0.226
delta_Rv0954	0.017	0.287
PonA1	-0.015	0.184
EccD1_KO	0.204	0.526
EspI_KO	1.084	0.588
PE35_KO	0.268	-0.155
PPE68_KO	0.72	-0.256
glycerol2	0.31	0.128
lignocerate	0.723	0.38
oleate	0.169	0.468
phosphatidylcholine	0.132	0.462
acetate	-0.598	-0.878
glucAc	-0.154	-0.554
Rv0950ko	-0.567	-0.042
Rv1096ko	0.419	1.149
Rv3684ko	0.147	0.386
delta_otsA_trehalose	-0.022	-0.603