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 Rv3426/PPE58:

update plot	correlation	link to info on gene
Rv0048c/-	(cc=0.596)	info on Rv0048c/-
Rv0220/lipC	(cc=0.5171)	info on Rv0220/lipC
Rv3379c/dxs2	(cc=0.5085)	info on Rv3379c/dxs2
Rv0246/-	(cc=0.4648)	info on Rv0246/-
Rv3675/-	(cc=0.4638)	info on Rv3675/-
Rv2443/dctA	(cc=0.4626)	info on Rv2443/dctA
Rv3847/-	(cc=0.4536)	info on Rv3847/-
Rv0112/gca	(cc=0.444)	info on Rv0112/gca
Rv0138/-	(cc=0.4367)	info on Rv0138/-
Rv0822c/-	(cc=0.4339)	info on Rv0822c/-

Correlation of Rv3426/PPE58 with Rv0048c/-

Normalized LFCs for Rv3426/PPE58:
(description and provenance of datasets)

	Rv3426/PPE58	Rv0048c/-
Fe_supp_jason_reseq	-0.766	-0.608
low_pH_jason_reseq	-0.259	0.204
NO_jason_reseq	0.226	0.557
B6_jason_reseq	0.214	0.409
MHCII_jason_reseq	0.6	0.192
Isoniazid02	-0.146	-0.493
Rifampicin4	-0.558	-0.233
Ethambutol3	3.31	1.6
Meropenem3	-0.535	-0.174
Vancomycin16	-0.355	0.244
Rv2680_day32	0.276	0.472
H37Rv_KO_MarP	0.484	0.382
hypoxia_3wks	0.379	0.092
hypoxia_6wks	-0.157	1.065
glycerol	-0.948	-0.432
cholesterol	-0.066	-0.367
AJ	0.861	0.548
Bibs02	-0.457	-0.172
Bibs02c	-1.381	0.065
BL6	-0.462	0.282
BL6a	0.086	0.557
BXD01	0.823	0.742
BXD010	0.533	0.586
BXD011	0.369	1.182
BXD03	0.458	0.682
BXD04	0.054	0.598
BXD05	0.945	0.75
BXD06	0.536	1.169
BXD07	0.637	0.94
BXD08	-0.03	1.08
BXD09	1.094	0.662
CAST	0.379	0.534
CCcont	-0.213	-0.225
DS01	0.103	-0.566
DS02	0.047	-0.211
DS04	0.319	-0.042
DS0c	0.476	0.515
GP01	0.612	2.136
GP02	1.471	1.23
GP0c	0.913	1.334
NOD	0.534	0.182
NZO	0.643	1.269
PWK	0.5	0.888
H37Rv_KO_CtpC	-1.213	-0.73
H37Rv_KO_CtpD	1.473	0.404
H37Rv_KO_Rv1272	0.091	0.53
H37Rv_KO_SugABC	1.107	1.214
H37Rv_KO_MbtN	-0.096	0.647
Trans05	-0.402	-0.115
macrophage_unactivated	0.783	-0.098
IL1	-0.374	0.098
Rapamycin	0.267	0.068
Tcell	0.283	-0.046
GMCSF	-0.333	-0.465
IFNab	-0.091	-0.366
IFNg	0.593	0.029
IFNg_GMCSF1	3.142	0.349
Rv1432_day32	0.763	1.12
Rv1565c_day32	-0.218	-0.302
secA2_input	-0.77	-0.421
delta_Rv3594	-0.493	-0.529
delta_Rv3717	-0.927	0.049
delta_Rv3811	-0.178	-0.049
delta_Rv0954	-1.292	0.059
PonA1	0.358	-0.508
EccD1_KO	-1.365	0.099
EspI_KO	-0.776	-0.257
PE35_KO	-0.639	-0.467
PPE68_KO	-1.139	-0.365
glycerol2	-0.545	0.228
lignocerate	-0.947	-0.111
oleate	0.111	0.666
phosphatidylcholine	-0.115	0.238
acetate	-0.874	-0.761
glucAc	-1.209	-0.578
Rv0950ko	0.081	0.368
Rv1096ko	-0.826	0.036
Rv3684ko	0.088	0.95
delta_otsA_trehalose	-0.142	-0.86