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 Rv3478/PPE60:

update plot	correlation	link to info on gene
Rv3479/-	(cc=0.5427)	info on Rv3479/-
Rv1523/-	(cc=0.5356)	info on Rv1523/-
Rv2517c/-	(cc=0.507)	info on Rv2517c/-
Rv0888/-	(cc=0.491)	info on Rv0888/-
Rv2556c/-	(cc=0.4787)	info on Rv2556c/-
Rv2332/mez	(cc=0.4784)	info on Rv2332/mez
Rv1803c/PE_PGRS32	(cc=0.4726)	info on Rv1803c/PE_PGRS32
Rv3059/cyp136	(cc=0.4557)	info on Rv3059/cyp136
Rv2659c/-	(cc=0.4538)	info on Rv2659c/-
Rv0089/-	(cc=0.4531)	info on Rv0089/-

Correlation of Rv3478/PPE60 with Rv0888/-

Normalized LFCs for Rv3478/PPE60:
(description and provenance of datasets)

	Rv3478/PPE60	Rv0888/-
Fe_supp_jason_reseq	-0.627	-0.245
low_pH_jason_reseq	-0.31	0.04
NO_jason_reseq	-0.509	-0.284
B6_jason_reseq	-0.499	0.32
MHCII_jason_reseq	-0.12	0.175
Isoniazid02	0.259	-0.31
Rifampicin4	0.301	0.298
Ethambutol3	0.637	0.852
Meropenem3	-0.805	-0.719
Vancomycin16	-0.738	-0.257
Rv2680_day32	1.156	0.477
H37Rv_KO_MarP	0.94	0.477
hypoxia_3wks	-0.658	-0.275
hypoxia_6wks	-0.921	-0.196
glycerol	-1.76	-0.582
cholesterol	-1.858	-0.453
AJ	0.096	0.262
Bibs02	-0.326	0.309
Bibs02c	-0.577	-0.255
BL6	-0.581	0.675
BL6a	-0.561	0.207
BXD01	-0.462	0.515
BXD010	-0.15	0.482
BXD011	-0.452	0.18
BXD03	-1.083	0.136
BXD04	-0.275	0.58
BXD05	-0.065	0.473
BXD06	-0.698	0.378
BXD07	-0.392	0.392
BXD08	-0.414	0.764
BXD09	-1.048	0.353
CAST	0.048	0.389
CCcont	0.008	0.327
DS01	-0.802	0.188
DS02	-0.011	0.098
DS04	-0.346	0.178
DS0c	-0.57	0.28
GP01	0.232	0.667
GP02	-1.328	0.806
GP0c	-1.284	-0.262
NOD	0.911	0.825
NZO	0.182	0.019
PWK	0.206	0.837
H37Rv_KO_CtpC	-0.472	-0.198
H37Rv_KO_CtpD	-1.876	0.204
H37Rv_KO_Rv1272	-0.269	0.094
H37Rv_KO_SugABC	-0.099	-0.162
H37Rv_KO_MbtN	-0.243	0.042
Trans05	0.823	0.501
macrophage_unactivated	-1.054	0.038
IL1	-0.243	-0.421
Rapamycin	-0.252	-0.436
Tcell	-0.13	-0.101
GMCSF	-1.302	-0.285
IFNab	-0.441	-0.49
IFNg	-0.604	-0.016
IFNg_GMCSF1	-0.459	-0.509
Rv1432_day32	2.139	0.79
Rv1565c_day32	0.055	0.687
secA2_input	0.05	-0.402
delta_Rv3594	0.162	0.672
delta_Rv3717	0.258	0.586
delta_Rv3811	-0.399	0.626
delta_Rv0954	0.567	1.119
PonA1	0.92	1.309
EccD1_KO	0.799	0.589
EspI_KO	0.77	0.944
PE35_KO	1.047	0.683
PPE68_KO	0.893	0.918
glycerol2	-0.517	0.419
lignocerate	0.141	0.659
oleate	-0.164	0.193
phosphatidylcholine	1.605	0.45
acetate	-0.574	0.088
glucAc	-0.595	0.342
Rv0950ko	-0.467	0.736
Rv1096ko	-0.253	0.847
Rv3684ko	-0.478	0.547
delta_otsA_trehalose	-1.319	0.916