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 Rv0399c/lpqK:

update plot	correlation	link to info on gene
Rv0940c/-	(cc=0.6977)	info on Rv0940c/-
Rv0115/hddA	(cc=0.6841)	info on Rv0115/hddA
Rv3329/-	(cc=0.6616)	info on Rv3329/-
Rv1997/ctpF	(cc=0.658)	info on Rv1997/ctpF
Rv3191c/-	(cc=0.6372)	info on Rv3191c/-
Rv0968/-	(cc=0.6234)	info on Rv0968/-
Rv2738c/-	(cc=0.6205)	info on Rv2738c/-
Rv3291c/lrpA	(cc=0.6164)	info on Rv3291c/lrpA
Rv2313c/-	(cc=0.6091)	info on Rv2313c/-
Rv0342/iniA	(cc=0.578)	info on Rv0342/iniA

Correlation of Rv0399c/lpqK with Rv3329/-

Normalized LFCs for Rv0399c/lpqK:
(description and provenance of datasets)

	Rv0399c/lpqK	Rv3329/-
Fe_supp_jason_reseq	0.215	0.0
low_pH_jason_reseq	0.087	0.33
NO_jason_reseq	0.522	0.257
B6_jason_reseq	0.114	0.714
MHCII_jason_reseq	0.21	0.049
Isoniazid02	-3.51	-2.423
Rifampicin4	0.764	0.598
Ethambutol3	-2.908	-1.639
Meropenem3	-2.207	-2.211
Vancomycin16	-1.08	-0.947
Rv2680_day32	-0.648	-0.046
H37Rv_KO_MarP	-0.277	-0.354
hypoxia_3wks	0.375	0.323
hypoxia_6wks	1.054	0.418
glycerol	0.107	0.294
cholesterol	0.349	0.128
AJ	0.153	0.576
Bibs02	-0.076	0.114
Bibs02c	1.291	-0.471
BL6	-0.052	-0.095
BL6a	0.936	-0.357
BXD01	0.069	0.024
BXD010	0.39	-0.183
BXD011	-0.185	-0.136
BXD03	0.695	0.412
BXD04	0.244	-0.07
BXD05	0.488	0.47
BXD06	0.018	-0.013
BXD07	0.091	0.197
BXD08	0.444	0.321
BXD09	0.0	-0.079
CAST	0.062	0.28
CCcont	-0.127	-0.159
DS01	0.544	0.137
DS02	-0.121	0.444
DS04	0.966	0.035
DS0c	0.523	0.079
GP01	-0.144	0.022
GP02	-0.527	-0.011
GP0c	0.018	-0.716
NOD	1.193	-0.063
NZO	-0.027	0.656
PWK	0.129	0.459
H37Rv_KO_CtpC	0.086	-0.471
H37Rv_KO_CtpD	1.419	-0.278
H37Rv_KO_Rv1272	-0.079	-0.856
H37Rv_KO_SugABC	0.683	-0.375
H37Rv_KO_MbtN	0.215	-0.939
Trans05	0.052	-0.265
macrophage_unactivated	-0.363	-0.281
IL1	-0.78	0.098
Rapamycin	0.381	0.199
Tcell	0.176	-0.042
GMCSF	0.327	0.069
IFNab	-0.662	-0.375
IFNg	-0.051	0.088
IFNg_GMCSF1	0.443	0.041
Rv1432_day32	0.082	-0.288
Rv1565c_day32	0.269	0.627
secA2_input	0.312	0.343
delta_Rv3594	0.057	-0.314
delta_Rv3717	0.115	-0.258
delta_Rv3811	-0.028	-0.421
delta_Rv0954	-0.96	0.094
PonA1	-0.112	0.264
EccD1_KO	0.161	-0.428
EspI_KO	0.274	0.1
PE35_KO	0.236	-0.7
PPE68_KO	0.259	-0.115
glycerol2	0.238	0.113
lignocerate	0.524	0.244
oleate	0.631	0.658
phosphatidylcholine	0.496	0.314
acetate	0.535	-0.07
glucAc	0.349	-0.458
Rv0950ko	0.048	0.054
Rv1096ko	0.745	0.262
Rv3684ko	-0.321	-0.118
delta_otsA_trehalose	0.178	0.232