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 Rv2957/-:

update plot	correlation	link to info on gene
Rv3125c/PPE49	(cc=0.6276)	info on Rv3125c/PPE49
Rv1498c/-	(cc=0.5722)	info on Rv1498c/-
Rv2775/-	(cc=0.5567)	info on Rv2775/-
Rv1506c/-	(cc=0.5511)	info on Rv1506c/-
Rv1503c/-	(cc=0.551)	info on Rv1503c/-
Rv2777c/-	(cc=0.5378)	info on Rv2777c/-
Rv3142c/-	(cc=0.5116)	info on Rv3142c/-
Rv2807/-	(cc=0.5105)	info on Rv2807/-
Rv2452c/-	(cc=0.5068)	info on Rv2452c/-
Rv2428/ahpC	(cc=0.5063)	info on Rv2428/ahpC

Correlation of Rv2957/- with Rv2807/-

Normalized LFCs for Rv2957/-:
(description and provenance of datasets)

	Rv2957/-	Rv2807/-
Fe_supp_jason_reseq	0.507	-0.144
low_pH_jason_reseq	-0.46	-0.033
NO_jason_reseq	-0.018	0.294
B6_jason_reseq	0.052	-1.393
MHCII_jason_reseq	0.319	-0.457
Isoniazid02	-0.784	-0.937
Rifampicin4	0.417	-1.113
Ethambutol3	0.316	-0.028
Meropenem3	-0.769	-0.686
Vancomycin16	-0.17	-0.318
Rv2680_day32	0.675	1.111
H37Rv_KO_MarP	0.492	0.429
hypoxia_3wks	-0.12	-0.359
hypoxia_6wks	-0.236	-0.495
glycerol	-0.018	-0.282
cholesterol	-0.17	0.321
AJ	0.171	-0.363
Bibs02	-0.04	0.362
Bibs02c	0.399	1.188
BL6	0.256	0.668
BL6a	0.131	0.987
BXD01	0.434	0.761
BXD010	0.519	0.661
BXD011	0.322	-0.137
BXD03	0.536	0.076
BXD04	0.994	0.087
BXD05	0.11	0.039
BXD06	0.465	0.057
BXD07	0.422	0.505
BXD08	0.268	0.564
BXD09	0.49	0.02
CAST	0.347	0.284
CCcont	0.191	0.757
DS01	-0.123	-0.07
DS02	0.221	1.254
DS04	-0.228	0.562
DS0c	0.358	1.196
GP01	0.782	0.85
GP02	0.576	-0.389
GP0c	0.039	0.391
NOD	0.692	-0.169
NZO	-0.402	-0.487
PWK	0.395	-0.443
H37Rv_KO_CtpC	0.936	1.312
H37Rv_KO_CtpD	0.909	1.175
H37Rv_KO_Rv1272	1.143	1.986
H37Rv_KO_SugABC	0.842	1.246
H37Rv_KO_MbtN	0.76	1.011
Trans05	1.468	0.274
macrophage_unactivated	0.615	-0.322
IL1	-0.329	-0.356
Rapamycin	-0.307	-0.206
Tcell	-0.476	-1.212
GMCSF	-0.869	0.169
IFNab	-0.115	-0.698
IFNg	0.139	-0.567
IFNg_GMCSF1	-0.478	-0.104
Rv1432_day32	0.01	0.112
Rv1565c_day32	0.0	-0.193
secA2_input	0.114	-1.518
delta_Rv3594	0.061	-0.82
delta_Rv3717	-0.609	-1.514
delta_Rv3811	0.0	-0.754
delta_Rv0954	-0.561	-0.91
PonA1	-0.38	-1.415
EccD1_KO	0.51	1.181
EspI_KO	0.853	1.358
PE35_KO	1.103	0.435
PPE68_KO	0.745	1.225
glycerol2	0.303	-1.701
lignocerate	0.247	-0.955
oleate	0.251	-2.164
phosphatidylcholine	0.356	-1.364
acetate	-0.318	-1.647
glucAc	-0.209	-0.036
Rv0950ko	0.666	-0.642
Rv1096ko	-0.344	0.0
Rv3684ko	0.131	0.331
delta_otsA_trehalose	-0.462	-1.844