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 Rv2818c/-

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

	Rv3166c/-	Rv2818c/-
Fe_supp_jason_reseq	1.028	0.302
low_pH_jason_reseq	0.482	0.102
NO_jason_reseq	0.087	-0.213
B6_jason_reseq	-1.11	-0.127
MHCII_jason_reseq	-0.193	0.454
Isoniazid02	0.412	-0.105
Rifampicin4	-0.073	-0.563
Ethambutol3	0.501	-0.157
Meropenem3	0.214	0.02
Vancomycin16	0.21	0.313
Rv2680_day32	0.781	-0.316
H37Rv_KO_MarP	0.183	-0.391
hypoxia_3wks	0.0	0.215
hypoxia_6wks	-0.336	0.403
glycerol	0.803	-0.363
cholesterol	0.497	-0.229
AJ	0.861	0.084
Bibs02	-0.621	0.098
Bibs02c	1.303	0.418
BL6	1.769	0.654
BL6a	2.045	1.184
BXD01	1.207	1.252
BXD010	0.811	1.154
BXD011	1.128	1.407
BXD03	1.462	1.319
BXD04	1.549	1.015
BXD05	1.91	1.503
BXD06	1.378	1.44
BXD07	1.851	1.573
BXD08	1.11	1.417
BXD09	1.744	1.177
CAST	-0.284	0.596
CCcont	1.322	1.109
DS01	0.219	0.246
DS02	0.277	0.367
DS04	0.28	0.786
DS0c	0.082	0.19
GP01	-0.079	0.802
GP02	1.205	0.227
GP0c	0.694	1.034
NOD	1.009	0.197
NZO	-0.525	-0.152
PWK	-1.138	-0.578
H37Rv_KO_CtpC	1.129	1.643
H37Rv_KO_CtpD	2.225	2.194
H37Rv_KO_Rv1272	0.296	1.215
H37Rv_KO_SugABC	0.159	0.93
H37Rv_KO_MbtN	-0.22	0.158
Trans05	0.097	0.593
macrophage_unactivated	0.71	0.407
IL1	0.86	-0.11
Rapamycin	1.019	0.074
Tcell	0.248	0.381
GMCSF	0.158	1.323
IFNab	1.128	0.251
IFNg	0.115	0.604
IFNg_GMCSF1	1.439	-0.277
Rv1432_day32	0.931	0.846
Rv1565c_day32	0.035	0.445
secA2_input	-0.233	-0.495
delta_Rv3594	0.537	1.175
delta_Rv3717	-0.866	0.828
delta_Rv3811	-0.235	0.659
delta_Rv0954	-0.544	0.028
PonA1	-0.922	0.824
EccD1_KO	0.533	0.178
EspI_KO	0.639	0.767
PE35_KO	0.359	1.561
PPE68_KO	0.266	1.872
glycerol2	-0.319	-0.122
lignocerate	0.222	0.038
oleate	-0.323	-0.03
phosphatidylcholine	0.088	0.262
acetate	0.53	0.103
glucAc	0.233	-0.101
Rv0950ko	-1.101	-0.832
Rv1096ko	-1.143	-0.501
Rv3684ko	-0.789	-1.071
delta_otsA_trehalose	-0.826	0.459