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 Rv2853/PE_PGRS48:

update plot	correlation	link to info on gene
Rv2352c/PPE38	(cc=0.5372)	info on Rv2352c/PPE38
Rv3223c/sigH	(cc=0.5123)	info on Rv3223c/sigH
Rv3045/adhC	(cc=0.512)	info on Rv3045/adhC
Rv0940c/-	(cc=0.5046)	info on Rv0940c/-
Rv3142c/-	(cc=0.4999)	info on Rv3142c/-
Rv0072/-	(cc=0.4958)	info on Rv0072/-
Rv0160c/PE4	(cc=0.4773)	info on Rv0160c/PE4
Rv3814c/-	(cc=0.4734)	info on Rv3814c/-
Rv3397c/phyA	(cc=0.464)	info on Rv3397c/phyA
Rv1498c/-	(cc=0.4635)	info on Rv1498c/-

Correlation of Rv2853/PE_PGRS48 with Rv2352c/PPE38

Normalized LFCs for Rv2853/PE_PGRS48:
(description and provenance of datasets)

	Rv2853/PE_PGRS48	Rv2352c/PPE38
Fe_supp_jason_reseq	0.641	0.35
low_pH_jason_reseq	-0.269	-1.029
NO_jason_reseq	0.06	-0.491
B6_jason_reseq	-0.414	-0.488
MHCII_jason_reseq	-0.425	-0.46
Isoniazid02	-0.965	-1.043
Rifampicin4	0.095	-0.208
Ethambutol3	0.258	-0.882
Meropenem3	-1.22	-1.085
Vancomycin16	-0.788	-0.602
Rv2680_day32	-0.666	-0.611
H37Rv_KO_MarP	-0.206	-0.629
hypoxia_3wks	-0.335	-0.06
hypoxia_6wks	-0.72	-0.56
glycerol	0.587	0.532
cholesterol	0.29	0.575
AJ	0.881	0.321
Bibs02	0.199	0.203
Bibs02c	0.273	0.297
BL6	0.488	0.173
BL6a	0.462	0.425
BXD01	0.269	0.346
BXD010	0.324	-0.031
BXD011	0.519	-0.232
BXD03	0.679	0.503
BXD04	0.39	0.661
BXD05	0.242	0.358
BXD06	0.507	0.167
BXD07	0.494	0.22
BXD08	0.497	0.298
BXD09	0.213	0.376
CAST	0.475	0.235
CCcont	0.574	-0.032
DS01	0.24	0.267
DS02	-0.408	0.17
DS04	0.623	0.554
DS0c	0.0	0.179
GP01	-0.129	0.253
GP02	0.108	0.349
GP0c	-0.182	0.348
NOD	0.61	-0.184
NZO	0.344	0.393
PWK	0.078	0.06
H37Rv_KO_CtpC	0.235	0.169
H37Rv_KO_CtpD	0.174	0.659
H37Rv_KO_Rv1272	0.811	1.248
H37Rv_KO_SugABC	-0.084	0.005
H37Rv_KO_MbtN	0.659	0.457
Trans05	1.389	1.088
macrophage_unactivated	-0.262	0.511
IL1	-0.196	-0.11
Rapamycin	-0.227	0.037
Tcell	-0.381	-0.495
GMCSF	-0.404	0.533
IFNab	-0.435	0.054
IFNg	-0.043	0.088
IFNg_GMCSF1	-0.182	0.364
Rv1432_day32	-0.018	0.407
Rv1565c_day32	1.512	-0.141
secA2_input	-0.747	-0.626
delta_Rv3594	-0.017	0.583
delta_Rv3717	0.169	-0.374
delta_Rv3811	0.271	0.268
delta_Rv0954	-0.42	0.289
PonA1	0.667	0.085
EccD1_KO	0.0	-0.566
EspI_KO	0.493	-0.031
PE35_KO	0.175	0.105
PPE68_KO	-0.134	0.275
glycerol2	-0.078	0.167
lignocerate	0.444	-0.169
oleate	-0.016	-0.004
phosphatidylcholine	0.245	-0.224
acetate	0.053	-0.047
glucAc	0.15	0.016
Rv0950ko	0.283	0.277
Rv1096ko	0.654	-0.012
Rv3684ko	0.845	-0.134
delta_otsA_trehalose	0.127	0.184