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 Rv0932c/pstS2

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

	Rv0413/mutT3	Rv0932c/pstS2
Fe_supp_jason_reseq	-0.687	-0.226
low_pH_jason_reseq	0.184	0.065
NO_jason_reseq	1.16	0.315
B6_jason_reseq	2.963	0.937
MHCII_jason_reseq	-0.088	-0.494
Isoniazid02	-4.688	-1.042
Rifampicin4	-1.841	0.485
Ethambutol3	-2.768	-1.279
Meropenem3	-2.323	-1.144
Vancomycin16	-1.563	-0.605
Rv2680_day32	-0.505	0.893
H37Rv_KO_MarP	-0.124	-0.707
hypoxia_3wks	-0.136	0.152
hypoxia_6wks	0.374	0.487
glycerol	0.282	-0.097
cholesterol	0.467	-0.03
AJ	0.546	0.118
Bibs02	0.536	-0.118
Bibs02c	-0.133	-0.17
BL6	1.424	0.714
BL6a	0.425	0.664
BXD01	1.626	0.494
BXD010	0.521	0.668
BXD011	0.519	0.876
BXD03	0.464	0.862
BXD04	1.339	0.896
BXD05	0.23	1.086
BXD06	0.549	0.825
BXD07	1.134	0.659
BXD08	2.132	1.148
BXD09	0.909	0.715
CAST	3.293	1.051
CCcont	0.272	0.169
DS01	-0.277	0.354
DS02	-0.072	0.394
DS04	0.777	0.606
DS0c	-0.064	0.539
GP01	1.109	0.278
GP02	-0.691	0.279
GP0c	-0.017	0.189
NOD	0.835	0.719
NZO	0.803	0.584
PWK	1.805	1.178
H37Rv_KO_CtpC	1.129	0.138
H37Rv_KO_CtpD	-0.667	0.361
H37Rv_KO_Rv1272	-0.605	1.144
H37Rv_KO_SugABC	0.194	0.855
H37Rv_KO_MbtN	-0.309	0.752
Trans05	0.133	0.983
macrophage_unactivated	-1.162	0.344
IL1	-0.009	-0.101
Rapamycin	0.457	-0.071
Tcell	-0.358	-0.094
GMCSF	-0.29	0.465
IFNab	-0.529	-0.193
IFNg	0.615	0.575
IFNg_GMCSF1	0.757	0.157
Rv1432_day32	3.568	1.05
Rv1565c_day32	0.025	-0.578
secA2_input	0.429	0.11
delta_Rv3594	-0.274	0.057
delta_Rv3717	0.165	0.428
delta_Rv3811	-0.51	0.077
delta_Rv0954	-0.452	-0.019
PonA1	0.232	0.157
EccD1_KO	1.033	0.464
EspI_KO	-0.063	0.784
PE35_KO	-0.694	0.239
PPE68_KO	-0.541	0.304
glycerol2	0.324	0.44
lignocerate	0.362	0.168
oleate	-0.346	0.225
phosphatidylcholine	0.931	-0.311
acetate	-0.279	0.1
glucAc	-0.143	-0.166
Rv0950ko	1.33	0.036
Rv1096ko	1.607	-0.389
Rv3684ko	2.492	0.02
delta_otsA_trehalose	0.252	-0.266