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 Rv0134/ephF:

update plot	correlation	link to info on gene
Rv2914c/pknI	(cc=0.549)	info on Rv2914c/pknI
Rv3896c/-	(cc=0.5341)	info on Rv3896c/-
Rv0327c/cyp135A1	(cc=0.5183)	info on Rv0327c/cyp135A1
Rv3026c/-	(cc=0.504)	info on Rv3026c/-
Rv0530/-	(cc=0.4818)	info on Rv0530/-
Rv3786c/-	(cc=0.4778)	info on Rv3786c/-
Rv3522/ltp4	(cc=0.473)	info on Rv3522/ltp4
Rv0897c/-	(cc=0.4604)	info on Rv0897c/-
Rv0858c/dapC	(cc=0.4531)	info on Rv0858c/dapC
Rv0648/-	(cc=0.4515)	info on Rv0648/-

Correlation of Rv0134/ephF with Rv0327c/cyp135A1

Normalized LFCs for Rv0134/ephF:
(description and provenance of datasets)

	Rv0134/ephF	Rv0327c/cyp135A1
Fe_supp_jason_reseq	-0.568	0.12
low_pH_jason_reseq	-0.688	0.095
NO_jason_reseq	0.391	-0.433
B6_jason_reseq	0.413	1.032
MHCII_jason_reseq	0.941	2.121
Isoniazid02	-0.345	-0.463
Rifampicin4	0.0	-0.615
Ethambutol3	-0.461	-0.173
Meropenem3	0.271	-0.252
Vancomycin16	-0.273	-0.122
Rv2680_day32	-0.09	-0.688
H37Rv_KO_MarP	0.213	-0.086
hypoxia_3wks	-0.478	-0.55
hypoxia_6wks	-0.106	-0.403
glycerol	0.168	-0.455
cholesterol	-0.859	-0.52
AJ	0.077	0.605
Bibs02	-0.449	-0.242
Bibs02c	0.759	1.023
BL6	0.587	0.414
BL6a	0.639	0.393
BXD01	-0.265	-0.636
BXD010	-0.255	0.151
BXD011	0.421	-0.136
BXD03	0.226	-0.372
BXD04	-0.24	-0.573
BXD05	0.463	-0.44
BXD06	0.175	-0.367
BXD07	-0.048	-0.482
BXD08	0.152	-0.021
BXD09	0.292	-0.401
CAST	0.792	0.335
CCcont	-0.331	-0.308
DS01	0.229	0.108
DS02	0.249	-0.104
DS04	1.152	-0.514
DS0c	0.445	0.669
GP01	0.371	0.202
GP02	1.127	0.999
GP0c	0.279	-0.219
NOD	0.404	-0.22
NZO	0.345	-0.064
PWK	0.566	0.271
H37Rv_KO_CtpC	-0.114	-1.103
H37Rv_KO_CtpD	-0.348	-0.273
H37Rv_KO_Rv1272	-0.224	-0.778
H37Rv_KO_SugABC	0.588	-1.177
H37Rv_KO_MbtN	0.961	-0.902
Trans05	-0.302	-0.346
macrophage_unactivated	0.069	0.65
IL1	0.018	-0.341
Rapamycin	-0.034	-0.448
Tcell	0.072	0.222
GMCSF	1.098	0.481
IFNab	-0.121	0.245
IFNg	0.596	0.11
IFNg_GMCSF1	1.037	0.76
Rv1432_day32	0.224	0.0
Rv1565c_day32	0.188	0.398
secA2_input	0.297	-0.033
delta_Rv3594	-0.197	-0.791
delta_Rv3717	0.127	-0.268
delta_Rv3811	-0.132	-0.457
delta_Rv0954	-0.098	-0.16
PonA1	0.698	0.557
EccD1_KO	0.421	0.457
EspI_KO	-0.351	-0.094
PE35_KO	-0.621	0.362
PPE68_KO	-0.682	0.538
glycerol2	0.265	0.298
lignocerate	0.952	1.14
oleate	-0.6	-0.578
phosphatidylcholine	0.326	0.604
acetate	0.51	1.119
glucAc	0.706	0.696
Rv0950ko	0.986	1.173
Rv1096ko	1.692	0.627
Rv3684ko	1.657	0.96
delta_otsA_trehalose	-0.613	-1.732