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 Rv2954c/-:

update plot	correlation	link to info on gene
Rv2345/-	(cc=0.5093)	info on Rv2345/-
Rv3323c/moaX	(cc=0.5085)	info on Rv3323c/moaX
Rv1981c/nrdF1	(cc=0.5056)	info on Rv1981c/nrdF1
Rv3164c/moxR3	(cc=0.5047)	info on Rv3164c/moxR3
Rv2675c/-	(cc=0.5015)	info on Rv2675c/-
Rv1175c/fadH	(cc=0.4701)	info on Rv1175c/fadH
Rv2429/ahpD	(cc=0.4693)	info on Rv2429/ahpD
Rv2602/vapC41	(cc=0.4588)	info on Rv2602/vapC41
Rv0940c/-	(cc=0.4577)	info on Rv0940c/-
Rv1511/gmdA	(cc=0.4575)	info on Rv1511/gmdA

Correlation of Rv2954c/- with Rv1981c/nrdF1

Normalized LFCs for Rv2954c/-:
(description and provenance of datasets)

	Rv2954c/-	Rv1981c/nrdF1
Fe_supp_jason_reseq	0.18	0.204
low_pH_jason_reseq	-1.161	-1.022
NO_jason_reseq	-0.412	-0.417
B6_jason_reseq	-0.145	0.31
MHCII_jason_reseq	-0.033	0.087
Isoniazid02	-0.723	-0.639
Rifampicin4	0.241	0.143
Ethambutol3	-0.405	0.064
Meropenem3	-0.68	-0.466
Vancomycin16	-0.17	-0.456
Rv2680_day32	0.205	0.742
H37Rv_KO_MarP	-0.069	-0.333
hypoxia_3wks	-0.104	-0.646
hypoxia_6wks	0.052	-1.297
glycerol	0.439	0.089
cholesterol	-0.029	-0.384
AJ	-0.123	-0.012
Bibs02	-0.449	0.468
Bibs02c	-0.631	0.473
BL6	0.216	0.25
BL6a	0.263	0.443
BXD01	0.268	0.283
BXD010	0.447	0.295
BXD011	0.468	0.653
BXD03	0.66	0.455
BXD04	0.546	0.492
BXD05	0.644	0.397
BXD06	0.056	0.536
BXD07	0.194	0.277
BXD08	-0.063	-0.029
BXD09	0.494	0.417
CAST	-0.053	-0.012
CCcont	0.171	0.321
DS01	-0.062	0.301
DS02	-0.169	-0.028
DS04	0.222	0.025
DS0c	0.368	0.542
GP01	1.056	0.421
GP02	-0.374	0.603
GP0c	-0.138	0.365
NOD	0.812	0.667
NZO	0.012	-0.39
PWK	0.347	0.036
H37Rv_KO_CtpC	-0.465	0.101
H37Rv_KO_CtpD	0.501	0.44
H37Rv_KO_Rv1272	1.286	0.588
H37Rv_KO_SugABC	0.428	1.0
H37Rv_KO_MbtN	0.066	0.046
Trans05	0.423	0.555
macrophage_unactivated	-0.076	0.174
IL1	-0.641	0.294
Rapamycin	0.055	-0.157
Tcell	-0.394	0.111
GMCSF	-0.05	0.269
IFNab	-0.357	0.166
IFNg	0.206	0.059
IFNg_GMCSF1	1.178	0.273
Rv1432_day32	0.631	-0.155
Rv1565c_day32	0.605	-0.878
secA2_input	-0.775	-0.427
delta_Rv3594	0.083	-0.049
delta_Rv3717	-0.186	-0.31
delta_Rv3811	0.311	0.012
delta_Rv0954	0.075	0.231
PonA1	0.5	0.359
EccD1_KO	0.234	0.066
EspI_KO	0.482	0.103
PE35_KO	0.846	-0.108
PPE68_KO	0.419	0.032
glycerol2	1.092	0.965
lignocerate	0.822	0.958
oleate	1.143	1.048
phosphatidylcholine	1.049	0.957
acetate	0.007	0.258
glucAc	-0.026	0.183
Rv0950ko	0.223	0.663
Rv1096ko	-0.63	0.118
Rv3684ko	-0.082	-0.331
delta_otsA_trehalose	0.216	0.71