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 Rv3486/-:

update plot	correlation	link to info on gene
Rv3198A/-	(cc=0.4838)	info on Rv3198A/-
Rv1319c/-	(cc=0.4748)	info on Rv1319c/-
Rv3784/-	(cc=0.4409)	info on Rv3784/-
Rv1987/-	(cc=0.4316)	info on Rv1987/-
Rv0507/mmpL2	(cc=0.4169)	info on Rv0507/mmpL2
Rv1870c/-	(cc=0.4104)	info on Rv1870c/-
Rv3351c/-	(cc=0.4043)	info on Rv3351c/-
Rv1896c/-	(cc=0.403)	info on Rv1896c/-
Rv2127/ansP1	(cc=0.3989)	info on Rv2127/ansP1
Rv3010c/pfkA	(cc=0.3984)	info on Rv3010c/pfkA

Correlation of Rv3486/- with Rv3198A/-

Normalized LFCs for Rv3486/-:
(description and provenance of datasets)

	Rv3486/-	Rv3198A/-
Fe_supp_jason_reseq	0.379	0.079
low_pH_jason_reseq	-1.196	-0.888
NO_jason_reseq	-0.654	-0.562
B6_jason_reseq	-0.522	-0.557
MHCII_jason_reseq	0.388	-0.498
Isoniazid02	-0.111	0.732
Rifampicin4	-0.428	-0.682
Ethambutol3	0.708	0.316
Meropenem3	0.163	0.343
Vancomycin16	0.045	-0.146
Rv2680_day32	1.086	-0.341
H37Rv_KO_MarP	0.47	-0.056
hypoxia_3wks	0.02	-0.08
hypoxia_6wks	0.317	0.349
glycerol	-0.171	-1.66
cholesterol	-0.64	-0.806
AJ	-0.143	-0.015
Bibs02	-0.658	-0.179
Bibs02c	0.265	0.252
BL6	-0.247	-0.255
BL6a	0.255	0.079
BXD01	-0.221	0.208
BXD010	0.016	0.107
BXD011	-0.026	0.124
BXD03	-0.063	0.567
BXD04	-0.179	0.901
BXD05	0.516	-0.076
BXD06	-0.019	0.178
BXD07	0.258	0.253
BXD08	0.333	0.421
BXD09	-0.152	0.522
CAST	-0.314	-0.167
CCcont	0.042	0.092
DS01	-0.727	0.279
DS02	0.176	0.178
DS04	0.129	-0.03
DS0c	-0.506	0.423
GP01	-0.453	-0.331
GP02	-1.348	-2.099
GP0c	0.132	-0.014
NOD	0.024	-0.205
NZO	-0.643	-0.355
PWK	-0.028	0.247
H37Rv_KO_CtpC	-0.275	-0.265
H37Rv_KO_CtpD	1.131	-0.187
H37Rv_KO_Rv1272	0.57	0.468
H37Rv_KO_SugABC	0.427	0.75
H37Rv_KO_MbtN	0.653	0.802
Trans05	0.504	0.442
macrophage_unactivated	0.107	0.432
IL1	-0.181	0.386
Rapamycin	0.236	0.838
Tcell	-0.199	-0.235
GMCSF	0.174	1.215
IFNab	0.076	0.378
IFNg	0.168	0.176
IFNg_GMCSF1	0.255	0.575
Rv1432_day32	0.501	0.506
Rv1565c_day32	0.22	-0.044
secA2_input	0.202	0.186
delta_Rv3594	0.257	-0.239
delta_Rv3717	-0.161	-0.452
delta_Rv3811	-0.635	-1.016
delta_Rv0954	-0.074	-0.382
PonA1	-0.376	-0.184
EccD1_KO	-0.072	0.345
EspI_KO	0.619	0.103
PE35_KO	-0.265	-0.172
PPE68_KO	-0.061	-0.49
glycerol2	0.622	0.86
lignocerate	0.725	0.712
oleate	0.364	0.506
phosphatidylcholine	0.599	0.794
acetate	0.196	-0.183
glucAc	0.221	0.8
Rv0950ko	-0.13	1.01
Rv1096ko	-1.324	0.0
Rv3684ko	-0.832	0.131
delta_otsA_trehalose	0.23	-0.097