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 Rv3689/-:

update plot	correlation	link to info on gene
Rv1072/-	(cc=0.6562)	info on Rv1072/-
Rv1387/PPE20	(cc=0.6534)	info on Rv1387/PPE20
Rv3694c/-	(cc=0.6327)	info on Rv3694c/-
Rv1386/PE15	(cc=0.62)	info on Rv1386/PE15
Rv3419c/gcp	(cc=0.6172)	info on Rv3419c/gcp
Rv1616/-	(cc=0.6155)	info on Rv1616/-
Rv3142c/-	(cc=0.5926)	info on Rv3142c/-
Rv0932c/pstS2	(cc=0.5862)	info on Rv0932c/pstS2
Rv1488/-	(cc=0.5853)	info on Rv1488/-
Rv2456c/-	(cc=0.5823)	info on Rv2456c/-

Correlation of Rv3689/- with Rv1488/-

Normalized LFCs for Rv3689/-:
(description and provenance of datasets)

	Rv3689/-	Rv1488/-
Fe_supp_jason_reseq	-0.388	0.177
low_pH_jason_reseq	-1.681	-1.091
NO_jason_reseq	0.105	-0.053
B6_jason_reseq	0.499	0.089
MHCII_jason_reseq	-0.62	-0.209
Isoniazid02	-1.107	-1.899
Rifampicin4	0.495	0.623
Ethambutol3	0.951	-0.277
Meropenem3	-0.364	-0.646
Vancomycin16	-0.058	-0.777
Rv2680_day32	-0.811	0.748
H37Rv_KO_MarP	-1.24	-0.444
hypoxia_3wks	0.638	0.654
hypoxia_6wks	0.739	0.725
glycerol	-0.295	0.439
cholesterol	-0.2	-0.435
AJ	0.576	0.323
Bibs02	-0.311	0.621
Bibs02c	-0.073	-0.72
BL6	0.728	0.723
BL6a	0.844	0.276
BXD01	1.055	0.797
BXD010	0.8	0.533
BXD011	0.852	0.6
BXD03	1.454	0.392
BXD04	1.548	1.853
BXD05	1.047	0.724
BXD06	0.962	0.646
BXD07	1.026	0.813
BXD08	1.004	1.419
BXD09	0.486	0.966
CAST	1.677	0.407
CCcont	0.27	-0.018
DS01	-0.202	-0.84
DS02	0.044	-0.202
DS04	0.225	0.721
DS0c	-0.091	-0.317
GP01	0.821	0.468
GP02	0.096	0.659
GP0c	0.85	0.352
NOD	0.957	0.199
NZO	1.16	0.877
PWK	2.364	0.386
H37Rv_KO_CtpC	0.806	0.778
H37Rv_KO_CtpD	0.981	1.127
H37Rv_KO_Rv1272	0.967	0.943
H37Rv_KO_SugABC	1.067	0.466
H37Rv_KO_MbtN	1.472	0.016
Trans05	0.496	0.575
macrophage_unactivated	0.079	-0.644
IL1	-0.374	-0.139
Rapamycin	-0.997	-0.341
Tcell	0.508	-0.029
GMCSF	0.132	-0.496
IFNab	0.206	-0.215
IFNg	0.722	-0.283
IFNg_GMCSF1	0.452	-0.132
Rv1432_day32	1.172	1.222
Rv1565c_day32	-0.482	0.079
secA2_input	-0.488	1.046
delta_Rv3594	-0.58	-0.135
delta_Rv3717	-0.205	-0.461
delta_Rv3811	-0.21	-0.233
delta_Rv0954	-0.979	0.391
PonA1	-0.099	-0.403
EccD1_KO	0.122	0.158
EspI_KO	-0.217	-0.742
PE35_KO	0.295	0.347
PPE68_KO	0.208	0.186
glycerol2	0.27	-0.052
lignocerate	-0.029	0.298
oleate	0.717	1.141
phosphatidylcholine	-0.052	0.113
acetate	0.284	-0.485
glucAc	0.188	-0.085
Rv0950ko	0.202	0.492
Rv1096ko	0.85	0.244
Rv3684ko	0.799	0.626
delta_otsA_trehalose	-0.482	-0.687