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 Rv0413/mutT3:

update plot	correlation	link to info on gene
Rv0231/fadE4	(cc=0.6135)	info on Rv0231/fadE4
Rv3329/-	(cc=0.5844)	info on Rv3329/-
Rv0991c/-	(cc=0.5842)	info on Rv0991c/-
Rv0975c/fadE13	(cc=0.5633)	info on Rv0975c/fadE13
Rv0932c/pstS2	(cc=0.5549)	info on Rv0932c/pstS2
Rv0342/iniA	(cc=0.5504)	info on Rv0342/iniA
Rv0940c/-	(cc=0.5288)	info on Rv0940c/-
Rv3191c/-	(cc=0.5236)	info on Rv3191c/-
Rv0399c/lpqK	(cc=0.517)	info on Rv0399c/lpqK
Rv3397c/phyA	(cc=0.515)	info on Rv3397c/phyA

Correlation of Rv0413/mutT3 with Rv3191c/-

Normalized LFCs for Rv0413/mutT3:
(description and provenance of datasets)

	Rv0413/mutT3	Rv3191c/-
Fe_supp_jason_reseq	-0.687	-0.024
low_pH_jason_reseq	0.184	-0.37
NO_jason_reseq	1.16	-0.06
B6_jason_reseq	2.963	0.47
MHCII_jason_reseq	-0.088	0.448
Isoniazid02	-4.688	-1.929
Rifampicin4	-1.841	0.625
Ethambutol3	-2.768	-2.151
Meropenem3	-2.323	-0.361
Vancomycin16	-1.563	-0.907
Rv2680_day32	-0.505	0.071
H37Rv_KO_MarP	-0.124	0.409
hypoxia_3wks	-0.136	-0.395
hypoxia_6wks	0.374	-0.683
glycerol	0.282	-0.176
cholesterol	0.467	-0.111
AJ	0.546	0.424
Bibs02	0.536	0.283
Bibs02c	-0.133	0.57
BL6	1.424	-0.065
BL6a	0.425	0.716
BXD01	1.626	-0.167
BXD010	0.521	0.178
BXD011	0.519	0.436
BXD03	0.464	0.247
BXD04	1.339	0.221
BXD05	0.23	0.692
BXD06	0.549	0.452
BXD07	1.134	0.158
BXD08	2.132	0.253
BXD09	0.909	0.623
CAST	3.293	0.439
CCcont	0.272	0.151
DS01	-0.277	0.862
DS02	-0.072	0.285
DS04	0.777	1.062
DS0c	-0.064	0.292
GP01	1.109	0.304
GP02	-0.691	-0.484
GP0c	-0.017	-0.684
NOD	0.835	0.539
NZO	0.803	0.585
PWK	1.805	0.624
H37Rv_KO_CtpC	1.129	0.291
H37Rv_KO_CtpD	-0.667	0.08
H37Rv_KO_Rv1272	-0.605	0.547
H37Rv_KO_SugABC	0.194	0.526
H37Rv_KO_MbtN	-0.309	0.429
Trans05	0.133	0.094
macrophage_unactivated	-1.162	-0.174
IL1	-0.009	-0.047
Rapamycin	0.457	-0.169
Tcell	-0.358	-0.606
GMCSF	-0.29	0.013
IFNab	-0.529	0.287
IFNg	0.615	0.102
IFNg_GMCSF1	0.757	0.33
Rv1432_day32	3.568	0.316
Rv1565c_day32	0.025	-0.591
secA2_input	0.429	-0.632
delta_Rv3594	-0.274	-0.08
delta_Rv3717	0.165	-0.216
delta_Rv3811	-0.51	0.025
delta_Rv0954	-0.452	-0.26
PonA1	0.232	0.123
EccD1_KO	1.033	-0.217
EspI_KO	-0.063	0.371
PE35_KO	-0.694	0.082
PPE68_KO	-0.541	-0.189
glycerol2	0.324	-0.113
lignocerate	0.362	0.516
oleate	-0.346	-0.413
phosphatidylcholine	0.931	0.084
acetate	-0.279	0.57
glucAc	-0.143	0.485
Rv0950ko	1.33	0.109
Rv1096ko	1.607	0.38
Rv3684ko	2.492	0.301
delta_otsA_trehalose	0.252	-0.138