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 Rv1981c/nrdF1:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.6569)	info on Rv3738c/PPE66
Rv0872c/PE_PGRS15	(cc=0.5792)	info on Rv0872c/PE_PGRS15
Rv1503c/-	(cc=0.5223)	info on Rv1503c/-
Rv2777c/-	(cc=0.5204)	info on Rv2777c/-
Rv3158/nuoN	(cc=0.5191)	info on Rv3158/nuoN
Rv2459/-	(cc=0.5148)	info on Rv2459/-
Rv2954c/-	(cc=0.5056)	info on Rv2954c/-
Rv0114/gmhB	(cc=0.5018)	info on Rv0114/gmhB
Rv2276/cyp121	(cc=0.4983)	info on Rv2276/cyp121
Rv3232c/ppk2	(cc=0.4961)	info on Rv3232c/ppk2

Correlation of Rv1981c/nrdF1 with Rv3738c/PPE66

Normalized LFCs for Rv1981c/nrdF1:
(description and provenance of datasets)

	Rv1981c/nrdF1	Rv3738c/PPE66
Fe_supp_jason_reseq	0.204	-0.238
low_pH_jason_reseq	-1.022	-0.192
NO_jason_reseq	-0.417	-0.034
B6_jason_reseq	0.31	-0.216
MHCII_jason_reseq	0.087	0.063
Isoniazid02	-0.639	-0.949
Rifampicin4	0.143	-0.014
Ethambutol3	0.064	-0.585
Meropenem3	-0.466	-0.751
Vancomycin16	-0.456	-0.825
Rv2680_day32	0.742	0.525
H37Rv_KO_MarP	-0.333	0.365
hypoxia_3wks	-0.646	-0.363
hypoxia_6wks	-1.297	-0.716
glycerol	0.089	-0.75
cholesterol	-0.384	-0.871
AJ	-0.012	-0.491
Bibs02	0.468	0.042
Bibs02c	0.473	1.031
BL6	0.25	0.475
BL6a	0.443	0.947
BXD01	0.283	0.456
BXD010	0.295	0.395
BXD011	0.653	0.668
BXD03	0.455	0.155
BXD04	0.492	0.142
BXD05	0.397	0.452
BXD06	0.536	0.191
BXD07	0.277	0.205
BXD08	-0.029	0.124
BXD09	0.417	0.225
CAST	-0.012	-0.087
CCcont	0.321	0.094
DS01	0.301	-0.044
DS02	-0.028	0.03
DS04	0.025	0.215
DS0c	0.542	0.148
GP01	0.421	0.298
GP02	0.603	1.222
GP0c	0.365	0.739
NOD	0.667	0.182
NZO	-0.39	-0.624
PWK	0.036	0.134
H37Rv_KO_CtpC	0.101	0.718
H37Rv_KO_CtpD	0.44	1.243
H37Rv_KO_Rv1272	0.588	0.297
H37Rv_KO_SugABC	1.0	0.756
H37Rv_KO_MbtN	0.046	0.763
Trans05	0.555	0.529
macrophage_unactivated	0.174	0.496
IL1	0.294	0.605
Rapamycin	-0.157	0.178
Tcell	0.111	0.316
GMCSF	0.269	0.356
IFNab	0.166	0.018
IFNg	0.059	-0.128
IFNg_GMCSF1	0.273	-0.057
Rv1432_day32	-0.155	0.297
Rv1565c_day32	-0.878	-0.046
secA2_input	-0.427	0.46
delta_Rv3594	-0.049	-0.488
delta_Rv3717	-0.31	-0.881
delta_Rv3811	0.012	-0.892
delta_Rv0954	0.231	-0.198
PonA1	0.359	-0.443
EccD1_KO	0.066	-0.234
EspI_KO	0.103	-0.359
PE35_KO	-0.108	-0.327
PPE68_KO	0.032	-0.154
glycerol2	0.965	0.824
lignocerate	0.958	0.927
oleate	1.048	0.953
phosphatidylcholine	0.957	0.975
acetate	0.258	0.076
glucAc	0.183	0.269
Rv0950ko	0.663	0.458
Rv1096ko	0.118	-0.377
Rv3684ko	-0.331	-0.269
delta_otsA_trehalose	0.71	1.259