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 Rv3786c/-

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

	Rv0134/ephF	Rv3786c/-
Fe_supp_jason_reseq	-0.568	-0.2
low_pH_jason_reseq	-0.688	-0.03
NO_jason_reseq	0.391	-0.386
B6_jason_reseq	0.413	0.123
MHCII_jason_reseq	0.941	0.456
Isoniazid02	-0.345	-0.294
Rifampicin4	0.0	-0.255
Ethambutol3	-0.461	0.107
Meropenem3	0.271	0.046
Vancomycin16	-0.273	-0.342
Rv2680_day32	-0.09	-0.634
H37Rv_KO_MarP	0.213	0.477
hypoxia_3wks	-0.478	-0.191
hypoxia_6wks	-0.106	-0.441
glycerol	0.168	0.171
cholesterol	-0.859	0.142
AJ	0.077	0.008
Bibs02	-0.449	-0.419
Bibs02c	0.759	0.468
BL6	0.587	-0.53
BL6a	0.639	-0.089
BXD01	-0.265	-0.794
BXD010	-0.255	-0.615
BXD011	0.421	0.351
BXD03	0.226	-0.544
BXD04	-0.24	-0.909
BXD05	0.463	-0.295
BXD06	0.175	-0.566
BXD07	-0.048	-0.49
BXD08	0.152	-0.535
BXD09	0.292	-0.604
CAST	0.792	-0.043
CCcont	-0.331	-0.236
DS01	0.229	0.263
DS02	0.249	0.139
DS04	1.152	0.718
DS0c	0.445	0.597
GP01	0.371	-0.277
GP02	1.127	-0.395
GP0c	0.279	-0.339
NOD	0.404	0.607
NZO	0.345	0.142
PWK	0.566	0.179
H37Rv_KO_CtpC	-0.114	-0.379
H37Rv_KO_CtpD	-0.348	0.137
H37Rv_KO_Rv1272	-0.224	-0.536
H37Rv_KO_SugABC	0.588	0.194
H37Rv_KO_MbtN	0.961	-0.05
Trans05	-0.302	-0.125
macrophage_unactivated	0.069	-0.54
IL1	0.018	0.062
Rapamycin	-0.034	-0.064
Tcell	0.072	0.023
GMCSF	1.098	0.354
IFNab	-0.121	0.423
IFNg	0.596	-0.607
IFNg_GMCSF1	1.037	0.173
Rv1432_day32	0.224	-0.274
Rv1565c_day32	0.188	-1.112
secA2_input	0.297	0.235
delta_Rv3594	-0.197	-0.682
delta_Rv3717	0.127	-0.49
delta_Rv3811	-0.132	-0.083
delta_Rv0954	-0.098	-0.105
PonA1	0.698	0.26
EccD1_KO	0.421	0.0
EspI_KO	-0.351	-0.271
PE35_KO	-0.621	-0.478
PPE68_KO	-0.682	-0.342
glycerol2	0.265	0.434
lignocerate	0.952	1.033
oleate	-0.6	-0.118
phosphatidylcholine	0.326	0.549
acetate	0.51	0.637
glucAc	0.706	0.633
Rv0950ko	0.986	1.007
Rv1096ko	1.692	0.422
Rv3684ko	1.657	0.567
delta_otsA_trehalose	-0.613	-0.024