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 Rv2892c/PPE45:

update plot	correlation	link to info on gene
Rv0551c/fadD8	(cc=0.5185)	info on Rv0551c/fadD8
Rv2191/-	(cc=0.4812)	info on Rv2191/-
Rv0855/far	(cc=0.4759)	info on Rv0855/far
Rv0941c/-	(cc=0.4615)	info on Rv0941c/-
Rv1513/-	(cc=0.4592)	info on Rv1513/-
Rv0572c/-	(cc=0.4528)	info on Rv0572c/-
Rv1966/mce3A	(cc=0.4464)	info on Rv1966/mce3A
Rv1861/-	(cc=0.444)	info on Rv1861/-
Rv0589/mce2A	(cc=0.4417)	info on Rv0589/mce2A
Rv3378c/-	(cc=0.4331)	info on Rv3378c/-

Correlation of Rv2892c/PPE45 with Rv1966/mce3A

Normalized LFCs for Rv2892c/PPE45:
(description and provenance of datasets)

	Rv2892c/PPE45	Rv1966/mce3A
Fe_supp_jason_reseq	-0.267	-0.398
low_pH_jason_reseq	-0.482	-0.08
NO_jason_reseq	-0.192	0.152
B6_jason_reseq	-0.296	-1.454
MHCII_jason_reseq	0.057	-0.572
Isoniazid02	0.501	0.298
Rifampicin4	0.644	0.338
Ethambutol3	0.241	1.409
Meropenem3	0.478	0.295
Vancomycin16	0.592	0.414
Rv2680_day32	0.499	-0.197
H37Rv_KO_MarP	-0.277	-0.488
hypoxia_3wks	0.73	0.55
hypoxia_6wks	0.94	-0.096
glycerol	-0.506	-0.661
cholesterol	-0.862	-1.068
AJ	0.182	0.492
Bibs02	0.221	0.71
Bibs02c	-0.186	-0.665
BL6	0.487	0.755
BL6a	0.42	0.255
BXD01	0.656	-0.172
BXD010	0.4	0.623
BXD011	0.248	0.393
BXD03	0.348	0.258
BXD04	0.005	0.275
BXD05	0.253	-0.026
BXD06	0.672	0.379
BXD07	0.551	0.087
BXD08	0.863	0.807
BXD09	0.674	0.632
CAST	0.01	0.475
CCcont	0.129	-0.373
DS01	0.157	-0.294
DS02	-0.246	0.124
DS04	1.483	-0.344
DS0c	0.431	-0.748
GP01	0.387	0.793
GP02	0.964	0.979
GP0c	0.263	0.516
NOD	0.314	1.076
NZO	-0.15	-0.354
PWK	-0.502	0.405
H37Rv_KO_CtpC	-0.199	0.446
H37Rv_KO_CtpD	0.351	0.81
H37Rv_KO_Rv1272	0.386	0.965
H37Rv_KO_SugABC	0.38	-0.827
H37Rv_KO_MbtN	-0.27	1.179
Trans05	0.282	0.689
macrophage_unactivated	0.092	-0.145
IL1	0.039	-0.231
Rapamycin	-0.147	-0.046
Tcell	0.124	-0.15
GMCSF	-0.011	0.47
IFNab	-0.266	-0.26
IFNg	0.166	-0.061
IFNg_GMCSF1	-0.317	-0.119
Rv1432_day32	-0.613	0.176
Rv1565c_day32	0.659	0.366
secA2_input	0.02	0.485
delta_Rv3594	0.0	0.026
delta_Rv3717	-0.322	0.031
delta_Rv3811	-0.595	-0.451
delta_Rv0954	0.155	-0.997
PonA1	-0.182	0.255
EccD1_KO	0.71	0.737
EspI_KO	0.63	1.474
PE35_KO	-0.038	0.983
PPE68_KO	0.102	1.261
glycerol2	0.509	-0.38
lignocerate	0.349	-0.694
oleate	0.885	0.332
phosphatidylcholine	0.798	-0.181
acetate	-0.776	-1.044
glucAc	-0.792	-0.994
Rv0950ko	1.2	0.063
Rv1096ko	1.14	0.371
Rv3684ko	0.495	0.498
delta_otsA_trehalose	2.157	1.92