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 Rv0940c/-:

update plot	correlation	link to info on gene
Rv0399c/lpqK	(cc=0.6977)	info on Rv0399c/lpqK
Rv0934/pstS1	(cc=0.6869)	info on Rv0934/pstS1
Rv3397c/phyA	(cc=0.6497)	info on Rv3397c/phyA
Rv1489A/-	(cc=0.6464)	info on Rv1489A/-
Rv0115/hddA	(cc=0.6452)	info on Rv0115/hddA
Rv3191c/-	(cc=0.6145)	info on Rv3191c/-
Rv0932c/pstS2	(cc=0.6033)	info on Rv0932c/pstS2
Rv3508/PE_PGRS54	(cc=0.6027)	info on Rv3508/PE_PGRS54
Rv1498c/-	(cc=0.5976)	info on Rv1498c/-
Rv0342/iniA	(cc=0.5886)	info on Rv0342/iniA

Correlation of Rv0940c/- with Rv0399c/lpqK

Normalized LFCs for Rv0940c/-:
(description and provenance of datasets)

	Rv0940c/-	Rv0399c/lpqK
Fe_supp_jason_reseq	-0.546	0.215
low_pH_jason_reseq	-0.445	0.087
NO_jason_reseq	0.126	0.522
B6_jason_reseq	-0.989	0.114
MHCII_jason_reseq	-0.421	0.21
Isoniazid02	-4.434	-3.51
Rifampicin4	0.482	0.764
Ethambutol3	-3.779	-2.908
Meropenem3	-4.315	-2.207
Vancomycin16	-1.417	-1.08
Rv2680_day32	0.113	-0.648
H37Rv_KO_MarP	-0.255	-0.277
hypoxia_3wks	-0.841	0.375
hypoxia_6wks	0.754	1.054
glycerol	0.316	0.107
cholesterol	0.168	0.349
AJ	0.57	0.153
Bibs02	-1.015	-0.076
Bibs02c	-0.311	1.291
BL6	0.847	-0.052
BL6a	0.284	0.936
BXD01	0.715	0.069
BXD010	1.34	0.39
BXD011	0.711	-0.185
BXD03	0.332	0.695
BXD04	1.328	0.244
BXD05	0.263	0.488
BXD06	1.327	0.018
BXD07	1.065	0.091
BXD08	0.743	0.444
BXD09	0.917	0.0
CAST	0.754	0.062
CCcont	1.0	-0.127
DS01	0.719	0.544
DS02	0.736	-0.121
DS04	1.234	0.966
DS0c	-0.102	0.523
GP01	0.312	-0.144
GP02	-0.803	-0.527
GP0c	-0.446	0.018
NOD	0.469	1.193
NZO	1.52	-0.027
PWK	0.254	0.129
H37Rv_KO_CtpC	0.585	0.086
H37Rv_KO_CtpD	0.147	1.419
H37Rv_KO_Rv1272	1.095	-0.079
H37Rv_KO_SugABC	0.088	0.683
H37Rv_KO_MbtN	0.528	0.215
Trans05	0.895	0.052
macrophage_unactivated	-0.082	-0.363
IL1	-0.317	-0.78
Rapamycin	-0.16	0.381
Tcell	0.205	0.176
GMCSF	-0.137	0.327
IFNab	-1.868	-0.662
IFNg	-1.446	-0.051
IFNg_GMCSF1	-1.197	0.443
Rv1432_day32	1.249	0.082
Rv1565c_day32	0.692	0.269
secA2_input	-0.863	0.312
delta_Rv3594	-0.571	0.057
delta_Rv3717	-0.691	0.115
delta_Rv3811	-0.663	-0.028
delta_Rv0954	-1.222	-0.96
PonA1	-1.092	-0.112
EccD1_KO	0.089	0.161
EspI_KO	1.087	0.274
PE35_KO	0.522	0.236
PPE68_KO	0.65	0.259
glycerol2	1.375	0.238
lignocerate	2.046	0.524
oleate	-0.469	0.631
phosphatidylcholine	1.426	0.496
acetate	1.812	0.535
glucAc	1.613	0.349
Rv0950ko	-0.482	0.048
Rv1096ko	-0.115	0.745
Rv3684ko	-0.524	-0.321
delta_otsA_trehalose	0.254	0.178