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 Rv1948c/-:

update plot	correlation	link to info on gene
Rv3429/PPE59	(cc=0.5502)	info on Rv3429/PPE59
Rv1504c/-	(cc=0.5446)	info on Rv1504c/-
Rv3142c/-	(cc=0.5371)	info on Rv3142c/-
Rv2107/PE22	(cc=0.5334)	info on Rv2107/PE22
Rv2735c/-	(cc=0.5311)	info on Rv2735c/-
Rv2519/PE26	(cc=0.5278)	info on Rv2519/PE26
Rv2666/-	(cc=0.5261)	info on Rv2666/-
Rv2819c/-	(cc=0.5251)	info on Rv2819c/-
Rv2929/-	(cc=0.5198)	info on Rv2929/-
Rv2134c/-	(cc=0.5166)	info on Rv2134c/-

Correlation of Rv1948c/- with Rv3429/PPE59

Normalized LFCs for Rv1948c/-:
(description and provenance of datasets)

	Rv1948c/-	Rv3429/PPE59
Fe_supp_jason_reseq	-0.508	0.628
low_pH_jason_reseq	-0.206	0.202
NO_jason_reseq	0.887	-0.029
B6_jason_reseq	-2.506	-1.06
MHCII_jason_reseq	-1.292	0.265
Isoniazid02	-0.185	-0.125
Rifampicin4	-0.791	-0.566
Ethambutol3	1.612	1.225
Meropenem3	-0.38	1.438
Vancomycin16	0.361	0.215
Rv2680_day32	0.915	-0.23
H37Rv_KO_MarP	-0.123	0.346
hypoxia_3wks	0.219	0.0
hypoxia_6wks	-0.885	0.069
glycerol	-0.348	-1.568
cholesterol	0.064	-0.909
AJ	1.086	0.382
Bibs02	-0.817	-0.276
Bibs02c	1.984	0.412
BL6	1.445	1.223
BL6a	1.709	1.017
BXD01	0.512	1.398
BXD010	0.421	1.497
BXD011	0.163	1.714
BXD03	-0.513	0.988
BXD04	0.322	0.307
BXD05	0.991	1.232
BXD06	0.525	1.426
BXD07	0.707	1.178
BXD08	0.437	1.307
BXD09	0.152	1.463
CAST	-0.277	0.379
CCcont	1.509	0.942
DS01	0.571	0.77
DS02	0.321	0.668
DS04	1.292	1.026
DS0c	1.31	0.728
GP01	1.547	1.468
GP02	0.019	0.874
GP0c	1.727	1.149
NOD	-0.576	0.443
NZO	0.483	0.516
PWK	0.74	0.602
H37Rv_KO_CtpC	0.981	1.547
H37Rv_KO_CtpD	1.213	1.898
H37Rv_KO_Rv1272	1.702	0.86
H37Rv_KO_SugABC	0.706	1.451
H37Rv_KO_MbtN	1.766	0.74
Trans05	1.32	1.42
macrophage_unactivated	-0.521	0.417
IL1	0.0	0.658
Rapamycin	-0.856	-0.203
Tcell	-0.831	1.121
GMCSF	-0.053	-0.412
IFNab	-0.121	-0.411
IFNg	0.0	0.216
IFNg_GMCSF1	-0.126	-0.459
Rv1432_day32	0.117	0.09
Rv1565c_day32	-0.839	-1.088
secA2_input	-0.87	-0.399
delta_Rv3594	0.193	-0.722
delta_Rv3717	0.06	-0.812
delta_Rv3811	0.419	-0.366
delta_Rv0954	0.041	-0.397
PonA1	-0.058	-0.518
EccD1_KO	-0.493	0.224
EspI_KO	-0.687	0.408
PE35_KO	0.312	0.548
PPE68_KO	0.294	0.189
glycerol2	-0.233	0.426
lignocerate	0.216	0.591
oleate	0.211	0.417
phosphatidylcholine	0.127	0.916
acetate	0.514	0.472
glucAc	0.319	0.483
Rv0950ko	0.217	0.422
Rv1096ko	-1.342	-0.582
Rv3684ko	-2.319	-0.54
delta_otsA_trehalose	-0.785	0.083