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 Rv3885c/eccE2:

update plot	correlation	link to info on gene
Rv1500/-	(cc=0.6042)	info on Rv1500/-
Rv3153/nuoI	(cc=0.5769)	info on Rv3153/nuoI
Rv2430c/PPE41	(cc=0.5711)	info on Rv2430c/PPE41
Rv3429/PPE59	(cc=0.5608)	info on Rv3429/PPE59
Rv0989c/grcC2	(cc=0.5607)	info on Rv0989c/grcC2
Rv1059/-	(cc=0.5575)	info on Rv1059/-
Rv3151/nuoG	(cc=0.5486)	info on Rv3151/nuoG
Rv0059/-	(cc=0.5436)	info on Rv0059/-
Rv2584c/apt	(cc=0.5426)	info on Rv2584c/apt
Rv0822c/-	(cc=0.5404)	info on Rv0822c/-

Correlation of Rv3885c/eccE2 with Rv0059/-

Normalized LFCs for Rv3885c/eccE2:
(description and provenance of datasets)

	Rv3885c/eccE2	Rv0059/-
Fe_supp_jason_reseq	0.44	0.371
low_pH_jason_reseq	-0.385	-0.437
NO_jason_reseq	-0.533	-0.137
B6_jason_reseq	-0.165	0.277
MHCII_jason_reseq	0.452	-0.351
Isoniazid02	0.063	-0.655
Rifampicin4	-0.079	-0.49
Ethambutol3	0.102	0.512
Meropenem3	0.678	-0.248
Vancomycin16	0.114	-0.348
Rv2680_day32	0.511	0.427
H37Rv_KO_MarP	0.243	0.44
hypoxia_3wks	0.0	0.335
hypoxia_6wks	0.487	0.67
glycerol	0.462	-0.282
cholesterol	-0.15	-0.325
AJ	0.133	0.133
Bibs02	0.787	0.42
Bibs02c	0.844	0.258
BL6	1.101	0.922
BL6a	1.492	0.578
BXD01	0.643	0.581
BXD010	0.568	0.406
BXD011	1.032	0.991
BXD03	1.332	0.728
BXD04	0.432	0.934
BXD05	0.935	0.697
BXD06	1.031	1.04
BXD07	1.253	0.409
BXD08	0.896	0.702
BXD09	1.072	0.591
CAST	-0.289	0.24
CCcont	1.222	0.212
DS01	0.986	0.228
DS02	0.993	-0.055
DS04	-0.159	-0.025
DS0c	1.226	0.116
GP01	0.655	-0.056
GP02	1.569	-0.661
GP0c	0.559	0.179
NOD	-0.547	0.103
NZO	-0.295	0.238
PWK	1.04	0.497
H37Rv_KO_CtpC	1.193	0.3
H37Rv_KO_CtpD	1.848	1.255
H37Rv_KO_Rv1272	0.98	0.537
H37Rv_KO_SugABC	1.39	1.05
H37Rv_KO_MbtN	-0.544	0.639
Trans05	-0.135	0.521
macrophage_unactivated	-0.224	-0.051
IL1	0.0	0.012
Rapamycin	-0.129	-0.166
Tcell	0.046	0.27
GMCSF	0.512	0.063
IFNab	0.438	-0.06
IFNg	0.144	0.128
IFNg_GMCSF1	0.0	-0.154
Rv1432_day32	0.525	0.076
Rv1565c_day32	0.126	0.036
secA2_input	-0.56	-0.412
delta_Rv3594	-0.823	-0.798
delta_Rv3717	-0.836	-0.517
delta_Rv3811	-0.629	-0.825
delta_Rv0954	-0.506	-0.181
PonA1	-0.157	-0.713
EccD1_KO	0.585	-0.73
EspI_KO	0.143	-0.505
PE35_KO	-0.265	-0.543
PPE68_KO	0.118	-0.608
glycerol2	0.345	0.324
lignocerate	0.257	-0.012
oleate	0.058	0.284
phosphatidylcholine	0.14	0.28
acetate	-0.178	-0.125
glucAc	-0.111	-0.172
Rv0950ko	-0.362	0.205
Rv1096ko	0.087	-0.075
Rv3684ko	0.187	-0.305
delta_otsA_trehalose	0.833	0.039