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 Rv3026c/-

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

	Rv0134/ephF	Rv3026c/-
Fe_supp_jason_reseq	-0.568	-0.996
low_pH_jason_reseq	-0.688	-0.427
NO_jason_reseq	0.391	-0.116
B6_jason_reseq	0.413	-0.019
MHCII_jason_reseq	0.941	-0.106
Isoniazid02	-0.345	-1.052
Rifampicin4	0.0	1.107
Ethambutol3	-0.461	-0.834
Meropenem3	0.271	-1.204
Vancomycin16	-0.273	-0.061
Rv2680_day32	-0.09	0.44
H37Rv_KO_MarP	0.213	0.137
hypoxia_3wks	-0.478	-0.287
hypoxia_6wks	-0.106	-0.422
glycerol	0.168	0.285
cholesterol	-0.859	-0.383
AJ	0.077	0.218
Bibs02	-0.449	0.772
Bibs02c	0.759	0.59
BL6	0.587	-0.317
BL6a	0.639	0.032
BXD01	-0.265	-0.297
BXD010	-0.255	-0.527
BXD011	0.421	-0.227
BXD03	0.226	-0.759
BXD04	-0.24	0.495
BXD05	0.463	-0.483
BXD06	0.175	-0.257
BXD07	-0.048	-0.267
BXD08	0.152	-0.039
BXD09	0.292	-0.071
CAST	0.792	0.823
CCcont	-0.331	-0.356
DS01	0.229	0.659
DS02	0.249	0.758
DS04	1.152	0.814
DS0c	0.445	0.658
GP01	0.371	-0.115
GP02	1.127	1.055
GP0c	0.279	0.243
NOD	0.404	1.033
NZO	0.345	0.538
PWK	0.566	0.264
H37Rv_KO_CtpC	-0.114	0.508
H37Rv_KO_CtpD	-0.348	0.166
H37Rv_KO_Rv1272	-0.224	-0.624
H37Rv_KO_SugABC	0.588	0.941
H37Rv_KO_MbtN	0.961	-0.025
Trans05	-0.302	-1.423
macrophage_unactivated	0.069	-0.508
IL1	0.018	0.047
Rapamycin	-0.034	-0.187
Tcell	0.072	0.016
GMCSF	1.098	0.264
IFNab	-0.121	-0.505
IFNg	0.596	-0.414
IFNg_GMCSF1	1.037	0.456
Rv1432_day32	0.224	-0.186
Rv1565c_day32	0.188	0.123
secA2_input	0.297	-0.089
delta_Rv3594	-0.197	-0.385
delta_Rv3717	0.127	-0.02
delta_Rv3811	-0.132	-0.294
delta_Rv0954	-0.098	-0.337
PonA1	0.698	0.463
EccD1_KO	0.421	0.332
EspI_KO	-0.351	0.382
PE35_KO	-0.621	0.391
PPE68_KO	-0.682	0.029
glycerol2	0.265	0.626
lignocerate	0.952	0.597
oleate	-0.6	0.241
phosphatidylcholine	0.326	0.695
acetate	0.51	0.218
glucAc	0.706	0.176
Rv0950ko	0.986	0.694
Rv1096ko	1.692	0.811
Rv3684ko	1.657	1.077
delta_otsA_trehalose	-0.613	-2.21