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 Rv0115/hddA:

update plot	correlation	link to info on gene
Rv0399c/lpqK	(cc=0.6841)	info on Rv0399c/lpqK
Rv0940c/-	(cc=0.6452)	info on Rv0940c/-
Rv0194/-	(cc=0.6193)	info on Rv0194/-
Rv1501/-	(cc=0.6143)	info on Rv1501/-
Rv0160c/PE4	(cc=0.5854)	info on Rv0160c/PE4
Rv0342/iniA	(cc=0.5757)	info on Rv0342/iniA
Rv3508/PE_PGRS54	(cc=0.5622)	info on Rv3508/PE_PGRS54
Rv3329/-	(cc=0.553)	info on Rv3329/-
Rv0343/iniC	(cc=0.5332)	info on Rv0343/iniC
Rv3191c/-	(cc=0.5259)	info on Rv3191c/-

Correlation of Rv0115/hddA with Rv0399c/lpqK

Normalized LFCs for Rv0115/hddA:
(description and provenance of datasets)

	Rv0115/hddA	Rv0399c/lpqK
Fe_supp_jason_reseq	-0.505	0.215
low_pH_jason_reseq	0.028	0.087
NO_jason_reseq	0.478	0.522
B6_jason_reseq	0.344	0.114
MHCII_jason_reseq	0.484	0.21
Isoniazid02	-2.546	-3.51
Rifampicin4	0.495	0.764
Ethambutol3	-2.227	-2.908
Meropenem3	-1.848	-2.207
Vancomycin16	-0.921	-1.08
Rv2680_day32	0.104	-0.648
H37Rv_KO_MarP	0.574	-0.277
hypoxia_3wks	0.152	0.375
hypoxia_6wks	0.906	1.054
glycerol	0.521	0.107
cholesterol	0.021	0.349
AJ	0.333	0.153
Bibs02	-0.864	-0.076
Bibs02c	0.191	1.291
BL6	-0.218	-0.052
BL6a	0.453	0.936
BXD01	0.17	0.069
BXD010	0.323	0.39
BXD011	-0.463	-0.185
BXD03	0.159	0.695
BXD04	0.0	0.244
BXD05	0.0	0.488
BXD06	-0.165	0.018
BXD07	0.19	0.091
BXD08	0.173	0.444
BXD09	0.128	0.0
CAST	-0.23	0.062
CCcont	0.064	-0.127
DS01	0.609	0.544
DS02	0.284	-0.121
DS04	0.489	0.966
DS0c	-0.148	0.523
GP01	0.468	-0.144
GP02	-0.338	-0.527
GP0c	0.469	0.018
NOD	-0.511	1.193
NZO	-0.136	-0.027
PWK	0.594	0.129
H37Rv_KO_CtpC	-0.37	0.086
H37Rv_KO_CtpD	1.079	1.419
H37Rv_KO_Rv1272	0.109	-0.079
H37Rv_KO_SugABC	1.569	0.683
H37Rv_KO_MbtN	-0.653	0.215
Trans05	0.575	0.052
macrophage_unactivated	0.11	-0.363
IL1	-0.747	-0.78
Rapamycin	-0.709	0.381
Tcell	0.417	0.176
GMCSF	-0.61	0.327
IFNab	-0.514	-0.662
IFNg	0.139	-0.051
IFNg_GMCSF1	-0.694	0.443
Rv1432_day32	0.029	0.082
Rv1565c_day32	-0.36	0.269
secA2_input	-0.517	0.312
delta_Rv3594	-0.448	0.057
delta_Rv3717	-0.96	0.115
delta_Rv3811	-0.629	-0.028
delta_Rv0954	-0.366	-0.96
PonA1	-0.806	-0.112
EccD1_KO	-1.246	0.161
EspI_KO	-0.422	0.274
PE35_KO	-0.627	0.236
PPE68_KO	-0.659	0.259
glycerol2	0.332	0.238
lignocerate	0.544	0.524
oleate	0.072	0.631
phosphatidylcholine	0.392	0.496
acetate	0.258	0.535
glucAc	0.389	0.349
Rv0950ko	0.241	0.048
Rv1096ko	-0.642	0.745
Rv3684ko	-1.055	-0.321
delta_otsA_trehalose	-0.019	0.178