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 Rv1889c/-:

update plot	correlation	link to info on gene
Rv2789c/fadE21	(cc=0.5487)	info on Rv2789c/fadE21
Rv0028/-	(cc=0.5288)	info on Rv0028/-
Rv3524/-	(cc=0.5119)	info on Rv3524/-
Rv0246/-	(cc=0.5104)	info on Rv0246/-
Rv2430c/PPE41	(cc=0.505)	info on Rv2430c/PPE41
Rv1176c/-	(cc=0.4965)	info on Rv1176c/-
Rv1021/-	(cc=0.4961)	info on Rv1021/-
Rv3150/nuoF	(cc=0.4898)	info on Rv3150/nuoF
Rv1059/-	(cc=0.4857)	info on Rv1059/-
Rv1500/-	(cc=0.4801)	info on Rv1500/-

Correlation of Rv1889c/- with Rv0028/-

Normalized LFCs for Rv1889c/-:
(description and provenance of datasets)

	Rv1889c/-	Rv0028/-
Fe_supp_jason_reseq	-0.237	-0.319
low_pH_jason_reseq	-0.223	-1.246
NO_jason_reseq	-1.515	0.273
B6_jason_reseq	-0.589	-0.253
MHCII_jason_reseq	-2.209	-0.418
Isoniazid02	0.201	0.102
Rifampicin4	0.298	-0.349
Ethambutol3	-0.302	-0.185
Meropenem3	-0.397	-0.037
Vancomycin16	0.061	0.082
Rv2680_day32	-0.119	0.862
H37Rv_KO_MarP	0.55	0.158
hypoxia_3wks	-0.53	-0.383
hypoxia_6wks	-0.378	-0.136
glycerol	-2.319	-1.871
cholesterol	-2.203	-1.108
AJ	-1.377	-1.257
Bibs02	-0.348	-0.184
Bibs02c	0.174	0.099
BL6	0.792	1.642
BL6a	1.4	1.119
BXD01	0.654	1.186
BXD010	1.514	1.693
BXD011	1.527	0.977
BXD03	1.267	1.352
BXD04	-0.113	1.079
BXD05	2.079	1.093
BXD06	0.833	1.113
BXD07	0.809	1.346
BXD08	0.94	1.232
BXD09	1.286	1.227
CAST	1.436	0.325
CCcont	1.016	1.792
DS01	0.236	0.128
DS02	0.217	0.785
DS04	-2.129	-1.078
DS0c	1.435	0.017
GP01	1.731	1.26
GP02	0.069	1.64
GP0c	0.521	-0.064
NOD	0.646	0.958
NZO	-1.589	0.53
PWK	0.163	-0.396
H37Rv_KO_CtpC	-1.783	-0.221
H37Rv_KO_CtpD	2.528	1.855
H37Rv_KO_Rv1272	2.005	0.476
H37Rv_KO_SugABC	-1.756	1.616
H37Rv_KO_MbtN	-0.359	-0.531
Trans05	1.798	0.307
macrophage_unactivated	2.834	0.013
IL1	-0.128	1.154
Rapamycin	0.252	0.608
Tcell	-1.75	-0.306
GMCSF	0.385	0.726
IFNab	2.001	0.457
IFNg	1.449	0.011
IFNg_GMCSF1	1.159	0.924
Rv1432_day32	-1.328	1.644
Rv1565c_day32	-1.275	-0.94
secA2_input	-0.031	0.416
delta_Rv3594	-1.632	0.018
delta_Rv3717	-0.084	-0.244
delta_Rv3811	-0.755	-1.258
delta_Rv0954	0.226	0.039
PonA1	-0.268	0.007
EccD1_KO	-2.375	0.069
EspI_KO	-0.918	-0.553
PE35_KO	-0.971	-0.082
PPE68_KO	-1.565	-0.045
glycerol2	0.209	0.406
lignocerate	0.43	0.897
oleate	-0.871	-0.418
phosphatidylcholine	0.078	0.318
acetate	-0.198	0.73
glucAc	0.759	0.533
Rv0950ko	0.356	0.567
Rv1096ko	-1.285	0.437
Rv3684ko	-0.111	0.18
delta_otsA_trehalose	-0.016	1.104