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 Rv1667c/-:

update plot	correlation	link to info on gene
Rv2730/-	(cc=0.4737)	info on Rv2730/-
Rv2568c/-	(cc=0.4511)	info on Rv2568c/-
Rv2134c/-	(cc=0.4495)	info on Rv2134c/-
Rv1886c/fbpB	(cc=0.4388)	info on Rv1886c/fbpB
Rv1364c/-	(cc=0.4356)	info on Rv1364c/-
Rv2886c/-	(cc=0.4301)	info on Rv2886c/-
Rv3818/-	(cc=0.4265)	info on Rv3818/-
Rv3305c/amiA1	(cc=0.4225)	info on Rv3305c/amiA1
Rv0999/-	(cc=0.4204)	info on Rv0999/-
Rv3050c/-	(cc=0.4194)	info on Rv3050c/-

Correlation of Rv1667c/- with Rv2886c/-

Normalized LFCs for Rv1667c/-:
(description and provenance of datasets)

	Rv1667c/-	Rv2886c/-
Fe_supp_jason_reseq	0.344	-0.802
low_pH_jason_reseq	-0.241	-0.748
NO_jason_reseq	0.176	-0.024
B6_jason_reseq	-1.077	-0.97
MHCII_jason_reseq	0.53	-0.025
Isoniazid02	0.473	-0.249
Rifampicin4	-0.658	-0.027
Ethambutol3	-0.213	0.0
Meropenem3	-0.404	-0.407
Vancomycin16	-0.464	-0.082
Rv2680_day32	1.135	0.156
H37Rv_KO_MarP	-0.538	-0.605
hypoxia_3wks	0.861	0.0
hypoxia_6wks	0.491	0.271
glycerol	1.321	0.467
cholesterol	0.01	0.134
AJ	0.297	-0.321
Bibs02	0.709	0.715
Bibs02c	0.182	0.067
BL6	0.369	1.083
BL6a	0.479	0.637
BXD01	0.428	0.747
BXD010	0.363	0.636
BXD011	0.54	1.003
BXD03	0.407	0.191
BXD04	0.863	0.185
BXD05	0.373	0.603
BXD06	0.651	0.645
BXD07	0.9	0.64
BXD08	1.084	1.17
BXD09	0.462	1.048
CAST	-0.239	-0.05
CCcont	0.889	1.007
DS01	-0.091	0.243
DS02	0.578	-0.555
DS04	0.236	0.398
DS0c	0.096	0.405
GP01	1.166	-0.112
GP02	0.274	0.368
GP0c	0.689	-0.148
NOD	0.584	-0.073
NZO	0.131	-0.179
PWK	-0.091	-0.199
H37Rv_KO_CtpC	0.153	0.431
H37Rv_KO_CtpD	0.444	0.952
H37Rv_KO_Rv1272	1.011	0.562
H37Rv_KO_SugABC	-0.207	0.733
H37Rv_KO_MbtN	-0.178	-0.155
Trans05	1.45	0.577
macrophage_unactivated	0.363	0.574
IL1	0.504	0.169
Rapamycin	0.792	0.147
Tcell	0.267	0.244
GMCSF	0.124	-0.293
IFNab	1.046	0.145
IFNg	0.032	0.078
IFNg_GMCSF1	-0.116	0.031
Rv1432_day32	0.369	0.313
Rv1565c_day32	-0.03	0.535
secA2_input	0.158	1.018
delta_Rv3594	0.233	0.136
delta_Rv3717	1.169	0.682
delta_Rv3811	0.404	0.59
delta_Rv0954	1.001	0.513
PonA1	0.671	0.217
EccD1_KO	0.405	0.263
EspI_KO	0.898	0.271
PE35_KO	0.583	0.939
PPE68_KO	0.47	0.637
glycerol2	-0.036	0.094
lignocerate	0.296	0.395
oleate	-1.136	-0.251
phosphatidylcholine	-0.31	0.27
acetate	0.475	0.111
glucAc	0.221	0.06
Rv0950ko	0.292	-0.093
Rv1096ko	-0.021	0.356
Rv3684ko	-0.655	0.049
delta_otsA_trehalose	-0.103	0.863