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 Rv1669/-:

update plot	correlation	link to info on gene
Rv3839/-	(cc=0.444)	info on Rv3839/-
Rv2352c/PPE38	(cc=0.4404)	info on Rv2352c/PPE38
Rv3438/-	(cc=0.4334)	info on Rv3438/-
Rv2162c/PE_PGRS38	(cc=0.3833)	info on Rv2162c/PE_PGRS38
Rv2973c/recG	(cc=0.3768)	info on Rv2973c/recG
Rv1563c/treY	(cc=0.372)	info on Rv1563c/treY
Rv1562c/treZ	(cc=0.364)	info on Rv1562c/treZ
Rv0255c/cobQ1	(cc=0.3627)	info on Rv0255c/cobQ1
Rv0423c/thiC	(cc=0.3537)	info on Rv0423c/thiC
Rv3742c/-	(cc=0.3512)	info on Rv3742c/-

Correlation of Rv1669/- with Rv2352c/PPE38

Normalized LFCs for Rv1669/-:
(description and provenance of datasets)

	Rv1669/-	Rv2352c/PPE38
Fe_supp_jason_reseq	0.824	0.35
low_pH_jason_reseq	-0.519	-1.029
NO_jason_reseq	-1.756	-0.491
B6_jason_reseq	0.0	-0.488
MHCII_jason_reseq	-0.421	-0.46
Isoniazid02	0.167	-1.043
Rifampicin4	-0.065	-0.208
Ethambutol3	-0.153	-0.882
Meropenem3	-0.151	-1.085
Vancomycin16	0.804	-0.602
Rv2680_day32	0.633	-0.611
H37Rv_KO_MarP	-0.601	-0.629
hypoxia_3wks	0.299	-0.06
hypoxia_6wks	-1.969	-0.56
glycerol	0.142	0.532
cholesterol	0.748	0.575
AJ	0.067	0.321
Bibs02	-0.38	0.203
Bibs02c	1.391	0.297
BL6	-0.45	0.173
BL6a	0.821	0.425
BXD01	-0.204	0.346
BXD010	-0.137	-0.031
BXD011	1.278	-0.232
BXD03	-0.06	0.503
BXD04	0.0	0.661
BXD05	0.884	0.358
BXD06	0.677	0.167
BXD07	0.257	0.22
BXD08	-0.164	0.298
BXD09	0.407	0.376
CAST	0.591	0.235
CCcont	0.164	-0.032
DS01	1.09	0.267
DS02	-0.233	0.17
DS04	1.681	0.554
DS0c	0.267	0.179
GP01	-0.508	0.253
GP02	0.547	0.349
GP0c	0.177	0.348
NOD	0.576	-0.184
NZO	0.621	0.393
PWK	0.524	0.06
H37Rv_KO_CtpC	-0.76	0.169
H37Rv_KO_CtpD	0.173	0.659
H37Rv_KO_Rv1272	1.483	1.248
H37Rv_KO_SugABC	0.029	0.005
H37Rv_KO_MbtN	-0.214	0.457
Trans05	1.157	1.088
macrophage_unactivated	1.035	0.511
IL1	-0.042	-0.11
Rapamycin	-0.703	0.037
Tcell	-0.433	-0.495
GMCSF	0.895	0.533
IFNab	0.33	0.054
IFNg	0.462	0.088
IFNg_GMCSF1	1.169	0.364
Rv1432_day32	0.074	0.407
Rv1565c_day32	0.444	-0.141
secA2_input	-0.171	-0.626
delta_Rv3594	0.0	0.583
delta_Rv3717	-0.287	-0.374
delta_Rv3811	0.611	0.268
delta_Rv0954	-0.093	0.289
PonA1	0.02	0.085
EccD1_KO	-0.566	-0.566
EspI_KO	-0.73	-0.031
PE35_KO	-0.16	0.105
PPE68_KO	1.075	0.275
glycerol2	-0.559	0.167
lignocerate	-0.296	-0.169
oleate	-0.345	-0.004
phosphatidylcholine	-0.071	-0.224
acetate	0.346	-0.047
glucAc	-0.08	0.016
Rv0950ko	0.766	0.277
Rv1096ko	0.856	-0.012
Rv3684ko	-0.187	-0.134
delta_otsA_trehalose	2.546	0.184