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 Rv1366/-

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

	Rv3522/ltp4	Rv1366/-
Fe_supp_jason_reseq	-0.17	-0.884
low_pH_jason_reseq	-0.097	-0.172
NO_jason_reseq	0.289	-0.294
B6_jason_reseq	-0.446	-0.871
MHCII_jason_reseq	0.866	-0.267
Isoniazid02	-0.511	0.148
Rifampicin4	-0.068	-0.376
Ethambutol3	0.068	0.269
Meropenem3	0.159	0.237
Vancomycin16	-0.202	0.172
Rv2680_day32	-1.285	-0.969
H37Rv_KO_MarP	0.134	0.518
hypoxia_3wks	-0.678	-0.235
hypoxia_6wks	-0.046	-0.048
glycerol	-0.508	-0.78
cholesterol	-0.439	-0.44
AJ	-0.682	0.134
Bibs02	-0.203	-0.823
Bibs02c	0.546	0.656
BL6	-0.62	0.376
BL6a	0.495	0.397
BXD01	-0.163	0.834
BXD010	0.202	1.115
BXD011	-0.208	0.35
BXD03	0.433	-0.278
BXD04	-0.385	0.315
BXD05	0.476	0.231
BXD06	-0.009	0.323
BXD07	0.31	0.476
BXD08	-0.081	0.506
BXD09	-0.451	-0.012
CAST	-0.759	-0.142
CCcont	0.114	0.646
DS01	-0.315	0.301
DS02	-0.493	-0.254
DS04	0.818	0.263
DS0c	0.097	0.525
GP01	0.451	1.227
GP02	0.793	1.296
GP0c	0.565	0.54
NOD	-0.952	0.148
NZO	0.14	0.839
PWK	-0.013	0.406
H37Rv_KO_CtpC	-1.024	0.467
H37Rv_KO_CtpD	-0.537	-0.907
H37Rv_KO_Rv1272	0.576	0.341
H37Rv_KO_SugABC	0.481	0.902
H37Rv_KO_MbtN	-0.285	0.392
Trans05	-0.145	0.557
macrophage_unactivated	-0.436	0.107
IL1	-0.86	-0.739
Rapamycin	-0.276	-0.681
Tcell	-0.036	0.694
GMCSF	0.114	-1.117
IFNab	0.033	-0.593
IFNg	-0.433	-1.384
IFNg_GMCSF1	0.427	-1.628
Rv1432_day32	-0.353	-0.55
Rv1565c_day32	0.829	0.175
secA2_input	0.845	-0.188
delta_Rv3594	-1.196	-0.249
delta_Rv3717	-0.95	0.371
delta_Rv3811	-0.761	-0.665
delta_Rv0954	-0.509	0.813
PonA1	-0.233	0.726
EccD1_KO	-0.194	-0.276
EspI_KO	0.046	0.262
PE35_KO	-0.569	0.379
PPE68_KO	-0.595	0.534
glycerol2	0.947	1.188
lignocerate	1.382	1.47
oleate	0.0	0.387
phosphatidylcholine	1.098	1.27
acetate	1.273	1.549
glucAc	0.994	1.226
Rv0950ko	1.055	0.856
Rv1096ko	0.651	0.32
Rv3684ko	0.707	0.534
delta_otsA_trehalose	0.066	1.077