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 Rv3896c/-

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

	Rv0134/ephF	Rv3896c/-
Fe_supp_jason_reseq	-0.568	-0.442
low_pH_jason_reseq	-0.688	-0.291
NO_jason_reseq	0.391	0.21
B6_jason_reseq	0.413	0.071
MHCII_jason_reseq	0.941	0.359
Isoniazid02	-0.345	-0.425
Rifampicin4	0.0	-0.103
Ethambutol3	-0.461	-0.119
Meropenem3	0.271	-0.229
Vancomycin16	-0.273	0.172
Rv2680_day32	-0.09	0.565
H37Rv_KO_MarP	0.213	0.389
hypoxia_3wks	-0.478	-0.55
hypoxia_6wks	-0.106	-0.288
glycerol	0.168	-0.48
cholesterol	-0.859	-0.775
AJ	0.077	-0.116
Bibs02	-0.449	-1.065
Bibs02c	0.759	0.729
BL6	0.587	0.319
BL6a	0.639	0.4
BXD01	-0.265	-0.628
BXD010	-0.255	-0.873
BXD011	0.421	-0.43
BXD03	0.226	-0.664
BXD04	-0.24	0.492
BXD05	0.463	-0.131
BXD06	0.175	-0.481
BXD07	-0.048	-0.621
BXD08	0.152	-0.236
BXD09	0.292	-0.343
CAST	0.792	-0.265
CCcont	-0.331	-0.304
DS01	0.229	-0.272
DS02	0.249	0.011
DS04	1.152	-0.131
DS0c	0.445	0.082
GP01	0.371	0.159
GP02	1.127	-0.09
GP0c	0.279	0.069
NOD	0.404	-0.708
NZO	0.345	0.246
PWK	0.566	-0.506
H37Rv_KO_CtpC	-0.114	-0.548
H37Rv_KO_CtpD	-0.348	0.401
H37Rv_KO_Rv1272	-0.224	0.132
H37Rv_KO_SugABC	0.588	-0.605
H37Rv_KO_MbtN	0.961	-0.317
Trans05	-0.302	-0.441
macrophage_unactivated	0.069	0.136
IL1	0.018	-0.053
Rapamycin	-0.034	0.433
Tcell	0.072	0.0
GMCSF	1.098	0.137
IFNab	-0.121	0.257
IFNg	0.596	-0.267
IFNg_GMCSF1	1.037	1.027
Rv1432_day32	0.224	-1.188
Rv1565c_day32	0.188	-0.494
secA2_input	0.297	0.765
delta_Rv3594	-0.197	-0.321
delta_Rv3717	0.127	-0.673
delta_Rv3811	-0.132	0.198
delta_Rv0954	-0.098	0.61
PonA1	0.698	0.0
EccD1_KO	0.421	-0.368
EspI_KO	-0.351	-0.913
PE35_KO	-0.621	-0.411
PPE68_KO	-0.682	-0.813
glycerol2	0.265	0.506
lignocerate	0.952	0.949
oleate	-0.6	-0.041
phosphatidylcholine	0.326	0.552
acetate	0.51	0.776
glucAc	0.706	1.004
Rv0950ko	0.986	1.309
Rv1096ko	1.692	1.046
Rv3684ko	1.657	1.235
delta_otsA_trehalose	-0.613	-1.658