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 Rv0160c/PE4:

update plot	correlation	link to info on gene
Rv0194/-	(cc=0.6467)	info on Rv0194/-
Rv0456B/mazE1	(cc=0.6442)	info on Rv0456B/mazE1
Rv0342/iniA	(cc=0.6199)	info on Rv0342/iniA
Rv3508/PE_PGRS54	(cc=0.6172)	info on Rv3508/PE_PGRS54
Rv0975c/fadE13	(cc=0.5938)	info on Rv0975c/fadE13
Rv2390c/-	(cc=0.5862)	info on Rv2390c/-
Rv0115/hddA	(cc=0.5854)	info on Rv0115/hddA
Rv2352c/PPE38	(cc=0.5845)	info on Rv2352c/PPE38
Rv3191c/-	(cc=0.5738)	info on Rv3191c/-
Rv0073/-	(cc=0.5614)	info on Rv0073/-

Correlation of Rv0160c/PE4 with Rv3508/PE_PGRS54

Normalized LFCs for Rv0160c/PE4:
(description and provenance of datasets)

	Rv0160c/PE4	Rv3508/PE_PGRS54
Fe_supp_jason_reseq	0.011	-0.532
low_pH_jason_reseq	-0.07	0.0
NO_jason_reseq	-0.11	0.0
B6_jason_reseq	0.416	-0.103
MHCII_jason_reseq	0.302	0.591
Isoniazid02	-1.8	-2.021
Rifampicin4	0.208	0.772
Ethambutol3	-0.931	-1.28
Meropenem3	-1.482	-1.748
Vancomycin16	-0.836	-0.727
Rv2680_day32	-0.088	0.046
H37Rv_KO_MarP	0.748	-0.103
hypoxia_3wks	-0.191	-0.215
hypoxia_6wks	-0.175	-0.616
glycerol	0.471	1.028
cholesterol	0.477	0.648
AJ	0.062	0.726
Bibs02	0.886	0.73
Bibs02c	0.584	0.415
BL6	0.188	-0.269
BL6a	0.375	0.27
BXD01	-0.029	0.259
BXD010	-0.023	-0.276
BXD011	0.241	-0.236
BXD03	0.15	-0.033
BXD04	0.354	0.03
BXD05	0.048	0.397
BXD06	0.316	0.182
BXD07	0.182	0.408
BXD08	0.338	0.947
BXD09	0.032	0.162
CAST	0.427	0.364
CCcont	-0.148	-0.193
DS01	0.281	-0.058
DS02	0.584	0.104
DS04	0.126	0.607
DS0c	-0.141	-0.28
GP01	0.358	1.149
GP02	1.382	1.255
GP0c	-0.229	1.092
NOD	0.364	-0.169
NZO	0.887	0.272
PWK	0.193	0.783
H37Rv_KO_CtpC	0.447	-0.209
H37Rv_KO_CtpD	1.091	0.441
H37Rv_KO_Rv1272	1.015	0.934
H37Rv_KO_SugABC	0.612	-0.243
H37Rv_KO_MbtN	0.485	0.184
Trans05	0.807	0.361
macrophage_unactivated	-0.354	-0.287
IL1	0.098	-0.365
Rapamycin	0.239	-1.126
Tcell	-0.248	-1.072
GMCSF	-0.09	-0.158
IFNab	0.039	-1.345
IFNg	0.294	-1.082
IFNg_GMCSF1	0.085	-0.698
Rv1432_day32	0.339	0.855
Rv1565c_day32	0.458	-0.52
secA2_input	-0.333	0.131
delta_Rv3594	-0.099	-0.402
delta_Rv3717	-0.239	-0.352
delta_Rv3811	-0.223	-0.269
delta_Rv0954	0.358	-1.151
PonA1	0.126	0.032
EccD1_KO	-0.444	-0.207
EspI_KO	0.074	0.043
PE35_KO	-0.446	-0.28
PPE68_KO	-0.221	-0.525
glycerol2	0.276	0.347
lignocerate	0.284	0.157
oleate	0.216	0.296
phosphatidylcholine	0.387	0.451
acetate	0.083	0.474
glucAc	0.264	0.753
Rv0950ko	0.479	-0.057
Rv1096ko	-0.13	0.226
Rv3684ko	0.134	-0.193
delta_otsA_trehalose	0.026	-0.026