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 Rv1616/-:

update plot	correlation	link to info on gene
Rv0822c/-	(cc=0.7063)	info on Rv0822c/-
Rv1752/-	(cc=0.6756)	info on Rv1752/-
Rv3151/nuoG	(cc=0.6467)	info on Rv3151/nuoG
Rv1918c/PPE35	(cc=0.644)	info on Rv1918c/PPE35
Rv3146/nuoB	(cc=0.6371)	info on Rv3146/nuoB
Rv1831/-	(cc=0.6352)	info on Rv1831/-
Rv3847/-	(cc=0.6327)	info on Rv3847/-
Rv3818/-	(cc=0.6282)	info on Rv3818/-
Rv3150/nuoF	(cc=0.6244)	info on Rv3150/nuoF
Rv1059/-	(cc=0.6182)	info on Rv1059/-

Correlation of Rv1616/- with Rv1752/-

Normalized LFCs for Rv1616/-:
(description and provenance of datasets)

	Rv1616/-	Rv1752/-
Fe_supp_jason_reseq	-0.396	0.898
low_pH_jason_reseq	-0.565	-0.161
NO_jason_reseq	0.48	-0.764
B6_jason_reseq	-0.844	-0.729
MHCII_jason_reseq	-0.966	-0.549
Isoniazid02	1.371	-0.434
Rifampicin4	1.162	0.555
Ethambutol3	1.67	1.171
Meropenem3	1.185	0.194
Vancomycin16	1.398	0.0
Rv2680_day32	0.079	-2.199
H37Rv_KO_MarP	-1.139	0.524
hypoxia_3wks	1.766	2.444
hypoxia_6wks	1.775	2.717
glycerol	1.251	1.779
cholesterol	1.032	0.643
AJ	1.133	1.076
Bibs02	0.539	0.404
Bibs02c	-0.621	-1.94
BL6	1.823	1.559
BL6a	1.778	2.314
BXD01	1.536	3.174
BXD010	2.447	1.471
BXD011	1.72	2.332
BXD03	2.456	2.639
BXD04	1.862	3.421
BXD05	2.644	3.019
BXD06	2.342	3.229
BXD07	2.289	2.882
BXD08	2.089	2.391
BXD09	2.112	2.702
CAST	1.021	0.779
CCcont	1.046	1.774
DS01	0.524	-1.437
DS02	0.46	-0.989
DS04	1.712	-0.544
DS0c	1.043	0.368
GP01	1.749	2.24
GP02	1.063	3.888
GP0c	1.472	2.7
NOD	-0.135	-0.142
NZO	1.017	1.621
PWK	1.576	0.117
H37Rv_KO_CtpC	2.035	2.829
H37Rv_KO_CtpD	0.541	1.947
H37Rv_KO_Rv1272	1.932	1.77
H37Rv_KO_SugABC	1.821	2.44
H37Rv_KO_MbtN	1.227	1.34
Trans05	2.0	-0.315
macrophage_unactivated	0.073	1.073
IL1	0.217	0.234
Rapamycin	0.175	1.197
Tcell	0.684	2.587
GMCSF	0.697	0.504
IFNab	1.149	-0.577
IFNg	0.783	-0.796
IFNg_GMCSF1	0.449	-0.346
Rv1432_day32	0.46	0.18
Rv1565c_day32	-1.071	-1.777
secA2_input	-0.928	0.44
delta_Rv3594	-0.578	0.646
delta_Rv3717	-0.642	-0.608
delta_Rv3811	-0.61	-0.802
delta_Rv0954	-0.735	1.056
PonA1	0.046	-0.6
EccD1_KO	0.418	0.842
EspI_KO	-0.471	0.625
PE35_KO	0.528	1.808
PPE68_KO	0.224	1.414
glycerol2	-0.339	-0.336
lignocerate	-1.159	-1.251
oleate	1.606	0.043
phosphatidylcholine	-0.305	-0.319
acetate	-0.788	-2.123
glucAc	-0.999	-1.959
Rv0950ko	0.32	0.142
Rv1096ko	-0.347	1.131
Rv3684ko	0.314	-0.976
delta_otsA_trehalose	-1.703	-2.184