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 Rv3522/ltp4:

update plot	correlation	link to info on gene
Rv0070c/glyA2	(cc=0.5126)	info on Rv0070c/glyA2
Rv3088/tgs4	(cc=0.4952)	info on Rv3088/tgs4
Rv0858c/dapC	(cc=0.4924)	info on Rv0858c/dapC
Rv2748c/ftsK	(cc=0.4866)	info on Rv2748c/ftsK
Rv3077/-	(cc=0.4833)	info on Rv3077/-
Rv1366/-	(cc=0.4772)	info on Rv1366/-
Rv1489A/-	(cc=0.4742)	info on Rv1489A/-
Rv0134/ephF	(cc=0.473)	info on Rv0134/ephF
Rv3081/-	(cc=0.4624)	info on Rv3081/-
Rv0312/-	(cc=0.4533)	info on Rv0312/-

Correlation of Rv3522/ltp4 with Rv0070c/glyA2

Normalized LFCs for Rv3522/ltp4:
(description and provenance of datasets)

	Rv3522/ltp4	Rv0070c/glyA2
Fe_supp_jason_reseq	-0.17	-0.096
low_pH_jason_reseq	-0.097	0.514
NO_jason_reseq	0.289	-0.079
B6_jason_reseq	-0.446	0.85
MHCII_jason_reseq	0.866	0.547
Isoniazid02	-0.511	0.109
Rifampicin4	-0.068	-0.636
Ethambutol3	0.068	1.521
Meropenem3	0.159	-0.393
Vancomycin16	-0.202	-0.172
Rv2680_day32	-1.285	-0.947
H37Rv_KO_MarP	0.134	0.185
hypoxia_3wks	-0.678	-0.459
hypoxia_6wks	-0.046	-0.43
glycerol	-0.508	0.099
cholesterol	-0.439	0.112
AJ	-0.682	-0.17
Bibs02	-0.203	0.305
Bibs02c	0.546	0.65
BL6	-0.62	1.125
BL6a	0.495	0.616
BXD01	-0.163	0.25
BXD010	0.202	0.407
BXD011	-0.208	-0.193
BXD03	0.433	0.711
BXD04	-0.385	0.084
BXD05	0.476	0.438
BXD06	-0.009	0.583
BXD07	0.31	0.578
BXD08	-0.081	0.642
BXD09	-0.451	0.457
CAST	-0.759	-0.269
CCcont	0.114	0.757
DS01	-0.315	0.27
DS02	-0.493	-0.23
DS04	0.818	1.366
DS0c	0.097	0.207
GP01	0.451	1.157
GP02	0.793	0.806
GP0c	0.565	0.354
NOD	-0.952	-0.473
NZO	0.14	-0.627
PWK	-0.013	0.473
H37Rv_KO_CtpC	-1.024	0.455
H37Rv_KO_CtpD	-0.537	0.458
H37Rv_KO_Rv1272	0.576	0.042
H37Rv_KO_SugABC	0.481	0.728
H37Rv_KO_MbtN	-0.285	-0.879
Trans05	-0.145	0.114
macrophage_unactivated	-0.436	0.271
IL1	-0.86	0.314
Rapamycin	-0.276	0.448
Tcell	-0.036	0.108
GMCSF	0.114	0.029
IFNab	0.033	0.59
IFNg	-0.433	0.115
IFNg_GMCSF1	0.427	0.99
Rv1432_day32	-0.353	0.353
Rv1565c_day32	0.829	-0.017
secA2_input	0.845	-0.288
delta_Rv3594	-1.196	-1.836
delta_Rv3717	-0.95	-1.057
delta_Rv3811	-0.761	-1.249
delta_Rv0954	-0.509	-1.186
PonA1	-0.233	-0.884
EccD1_KO	-0.194	-0.941
EspI_KO	0.046	-0.662
PE35_KO	-0.569	0.193
PPE68_KO	-0.595	-0.259
glycerol2	0.947	0.643
lignocerate	1.382	0.392
oleate	0.0	0.257
phosphatidylcholine	1.098	0.422
acetate	1.273	0.733
glucAc	0.994	0.901
Rv0950ko	1.055	0.507
Rv1096ko	0.651	1.104
Rv3684ko	0.707	0.55
delta_otsA_trehalose	0.066	-0.039