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 Rv3166c/-:

update plot	correlation	link to info on gene
Rv2452c/-	(cc=0.6893)	info on Rv2452c/-
Rv0501/galE2	(cc=0.6028)	info on Rv0501/galE2
Rv0371c/-	(cc=0.589)	info on Rv0371c/-
Rv2548/vapC19	(cc=0.5851)	info on Rv2548/vapC19
Rv2584c/apt	(cc=0.562)	info on Rv2584c/apt
Rv1831/-	(cc=0.5606)	info on Rv1831/-
Rv1505c/-	(cc=0.5566)	info on Rv1505c/-
Rv1583c/-	(cc=0.5531)	info on Rv1583c/-
Rv2500c/fadE19	(cc=0.5521)	info on Rv2500c/fadE19
Rv2818c/-	(cc=0.5391)	info on Rv2818c/-

Correlation of Rv3166c/- with Rv0371c/-

Normalized LFCs for Rv3166c/-:
(description and provenance of datasets)

	Rv3166c/-	Rv0371c/-
Fe_supp_jason_reseq	1.028	-0.439
low_pH_jason_reseq	0.482	-0.776
NO_jason_reseq	0.087	-0.614
B6_jason_reseq	-1.11	-1.467
MHCII_jason_reseq	-0.193	-1.383
Isoniazid02	0.412	0.201
Rifampicin4	-0.073	0.0
Ethambutol3	0.501	0.0
Meropenem3	0.214	0.0
Vancomycin16	0.21	0.366
Rv2680_day32	0.781	-0.363
H37Rv_KO_MarP	0.183	0.0
hypoxia_3wks	0.0	0.335
hypoxia_6wks	-0.336	-0.317
glycerol	0.803	0.385
cholesterol	0.497	-0.216
AJ	0.861	1.334
Bibs02	-0.621	-0.775
Bibs02c	1.303	1.914
BL6	1.769	4.166
BL6a	2.045	2.574
BXD01	1.207	2.329
BXD010	0.811	3.1
BXD011	1.128	2.844
BXD03	1.462	2.737
BXD04	1.549	1.656
BXD05	1.91	1.852
BXD06	1.378	1.957
BXD07	1.851	2.64
BXD08	1.11	1.702
BXD09	1.744	2.582
CAST	-0.284	2.478
CCcont	1.322	1.97
DS01	0.219	1.627
DS02	0.277	0.972
DS04	0.28	-0.628
DS0c	0.082	0.869
GP01	-0.079	0.067
GP02	1.205	2.203
GP0c	0.694	1.861
NOD	1.009	4.59
NZO	-0.525	0.6
PWK	-1.138	-0.142
H37Rv_KO_CtpC	1.129	0.309
H37Rv_KO_CtpD	2.225	0.0
H37Rv_KO_Rv1272	0.296	0.811
H37Rv_KO_SugABC	0.159	-0.321
H37Rv_KO_MbtN	-0.22	2.275
Trans05	0.097	0.459
macrophage_unactivated	0.71	0.227
IL1	0.86	0.214
Rapamycin	1.019	0.512
Tcell	0.248	0.326
GMCSF	0.158	0.895
IFNab	1.128	0.302
IFNg	0.115	-0.243
IFNg_GMCSF1	1.439	-0.591
Rv1432_day32	0.931	0.0
Rv1565c_day32	0.035	0.0
secA2_input	-0.233	-0.47
delta_Rv3594	0.537	-0.572
delta_Rv3717	-0.866	0.287
delta_Rv3811	-0.235	-1.096
delta_Rv0954	-0.544	-2.335
PonA1	-0.922	-1.928
EccD1_KO	0.533	-0.898
EspI_KO	0.639	-0.451
PE35_KO	0.359	-0.3
PPE68_KO	0.266	-0.163
glycerol2	-0.319	-0.97
lignocerate	0.222	0.0
oleate	-0.323	-2.741
phosphatidylcholine	0.088	-1.307
acetate	0.53	0.0
glucAc	0.233	0.0
Rv0950ko	-1.101	-1.122
Rv1096ko	-1.143	0.38
Rv3684ko	-0.789	-0.452
delta_otsA_trehalose	-0.826	0.0