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 Rv0399c/lpqK

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

	Rv0413/mutT3	Rv0399c/lpqK
Fe_supp_jason_reseq	-0.687	0.215
low_pH_jason_reseq	0.184	0.087
NO_jason_reseq	1.16	0.522
B6_jason_reseq	2.963	0.114
MHCII_jason_reseq	-0.088	0.21
Isoniazid02	-4.688	-3.51
Rifampicin4	-1.841	0.764
Ethambutol3	-2.768	-2.908
Meropenem3	-2.323	-2.207
Vancomycin16	-1.563	-1.08
Rv2680_day32	-0.505	-0.648
H37Rv_KO_MarP	-0.124	-0.277
hypoxia_3wks	-0.136	0.375
hypoxia_6wks	0.374	1.054
glycerol	0.282	0.107
cholesterol	0.467	0.349
AJ	0.546	0.153
Bibs02	0.536	-0.076
Bibs02c	-0.133	1.291
BL6	1.424	-0.052
BL6a	0.425	0.936
BXD01	1.626	0.069
BXD010	0.521	0.39
BXD011	0.519	-0.185
BXD03	0.464	0.695
BXD04	1.339	0.244
BXD05	0.23	0.488
BXD06	0.549	0.018
BXD07	1.134	0.091
BXD08	2.132	0.444
BXD09	0.909	0.0
CAST	3.293	0.062
CCcont	0.272	-0.127
DS01	-0.277	0.544
DS02	-0.072	-0.121
DS04	0.777	0.966
DS0c	-0.064	0.523
GP01	1.109	-0.144
GP02	-0.691	-0.527
GP0c	-0.017	0.018
NOD	0.835	1.193
NZO	0.803	-0.027
PWK	1.805	0.129
H37Rv_KO_CtpC	1.129	0.086
H37Rv_KO_CtpD	-0.667	1.419
H37Rv_KO_Rv1272	-0.605	-0.079
H37Rv_KO_SugABC	0.194	0.683
H37Rv_KO_MbtN	-0.309	0.215
Trans05	0.133	0.052
macrophage_unactivated	-1.162	-0.363
IL1	-0.009	-0.78
Rapamycin	0.457	0.381
Tcell	-0.358	0.176
GMCSF	-0.29	0.327
IFNab	-0.529	-0.662
IFNg	0.615	-0.051
IFNg_GMCSF1	0.757	0.443
Rv1432_day32	3.568	0.082
Rv1565c_day32	0.025	0.269
secA2_input	0.429	0.312
delta_Rv3594	-0.274	0.057
delta_Rv3717	0.165	0.115
delta_Rv3811	-0.51	-0.028
delta_Rv0954	-0.452	-0.96
PonA1	0.232	-0.112
EccD1_KO	1.033	0.161
EspI_KO	-0.063	0.274
PE35_KO	-0.694	0.236
PPE68_KO	-0.541	0.259
glycerol2	0.324	0.238
lignocerate	0.362	0.524
oleate	-0.346	0.631
phosphatidylcholine	0.931	0.496
acetate	-0.279	0.535
glucAc	-0.143	0.349
Rv0950ko	1.33	0.048
Rv1096ko	1.607	0.745
Rv3684ko	2.492	-0.321
delta_otsA_trehalose	0.252	0.178