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 Rv0160c/PE4

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

	Rv0115/hddA	Rv0160c/PE4
Fe_supp_jason_reseq	-0.505	0.011
low_pH_jason_reseq	0.028	-0.07
NO_jason_reseq	0.478	-0.11
B6_jason_reseq	0.344	0.416
MHCII_jason_reseq	0.484	0.302
Isoniazid02	-2.546	-1.8
Rifampicin4	0.495	0.208
Ethambutol3	-2.227	-0.931
Meropenem3	-1.848	-1.482
Vancomycin16	-0.921	-0.836
Rv2680_day32	0.104	-0.088
H37Rv_KO_MarP	0.574	0.748
hypoxia_3wks	0.152	-0.191
hypoxia_6wks	0.906	-0.175
glycerol	0.521	0.471
cholesterol	0.021	0.477
AJ	0.333	0.062
Bibs02	-0.864	0.886
Bibs02c	0.191	0.584
BL6	-0.218	0.188
BL6a	0.453	0.375
BXD01	0.17	-0.029
BXD010	0.323	-0.023
BXD011	-0.463	0.241
BXD03	0.159	0.15
BXD04	0.0	0.354
BXD05	0.0	0.048
BXD06	-0.165	0.316
BXD07	0.19	0.182
BXD08	0.173	0.338
BXD09	0.128	0.032
CAST	-0.23	0.427
CCcont	0.064	-0.148
DS01	0.609	0.281
DS02	0.284	0.584
DS04	0.489	0.126
DS0c	-0.148	-0.141
GP01	0.468	0.358
GP02	-0.338	1.382
GP0c	0.469	-0.229
NOD	-0.511	0.364
NZO	-0.136	0.887
PWK	0.594	0.193
H37Rv_KO_CtpC	-0.37	0.447
H37Rv_KO_CtpD	1.079	1.091
H37Rv_KO_Rv1272	0.109	1.015
H37Rv_KO_SugABC	1.569	0.612
H37Rv_KO_MbtN	-0.653	0.485
Trans05	0.575	0.807
macrophage_unactivated	0.11	-0.354
IL1	-0.747	0.098
Rapamycin	-0.709	0.239
Tcell	0.417	-0.248
GMCSF	-0.61	-0.09
IFNab	-0.514	0.039
IFNg	0.139	0.294
IFNg_GMCSF1	-0.694	0.085
Rv1432_day32	0.029	0.339
Rv1565c_day32	-0.36	0.458
secA2_input	-0.517	-0.333
delta_Rv3594	-0.448	-0.099
delta_Rv3717	-0.96	-0.239
delta_Rv3811	-0.629	-0.223
delta_Rv0954	-0.366	0.358
PonA1	-0.806	0.126
EccD1_KO	-1.246	-0.444
EspI_KO	-0.422	0.074
PE35_KO	-0.627	-0.446
PPE68_KO	-0.659	-0.221
glycerol2	0.332	0.276
lignocerate	0.544	0.284
oleate	0.072	0.216
phosphatidylcholine	0.392	0.387
acetate	0.258	0.083
glucAc	0.389	0.264
Rv0950ko	0.241	0.479
Rv1096ko	-0.642	-0.13
Rv3684ko	-1.055	0.134
delta_otsA_trehalose	-0.019	0.026