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 Rv2860c/glnA4:

update plot	correlation	link to info on gene
Rv0959/-	(cc=0.6171)	info on Rv0959/-
Rv3062/ligB	(cc=0.5403)	info on Rv3062/ligB
Rv3655c/-	(cc=0.5328)	info on Rv3655c/-
Rv2484c/-	(cc=0.5218)	info on Rv2484c/-
Rv1180/pks3	(cc=0.5176)	info on Rv1180/pks3
Rv2236c/cobD	(cc=0.5173)	info on Rv2236c/cobD
Rv0569/-	(cc=0.5139)	info on Rv0569/-
Rv3371/-	(cc=0.5112)	info on Rv3371/-
Rv3652/PE_PGRS60	(cc=0.4998)	info on Rv3652/PE_PGRS60
Rv2915c/-	(cc=0.499)	info on Rv2915c/-

Correlation of Rv2860c/glnA4 with Rv3371/-

Normalized LFCs for Rv2860c/glnA4:
(description and provenance of datasets)

	Rv2860c/glnA4	Rv3371/-
Fe_supp_jason_reseq	0.272	-0.442
low_pH_jason_reseq	0.348	-0.527
NO_jason_reseq	-0.163	-1.016
B6_jason_reseq	1.016	-0.131
MHCII_jason_reseq	1.38	1.576
Isoniazid02	0.528	1.059
Rifampicin4	-0.206	-0.125
Ethambutol3	2.104	0.518
Meropenem3	0.435	0.386
Vancomycin16	0.443	0.451
Rv2680_day32	0.795	-0.074
H37Rv_KO_MarP	-0.167	-0.151
hypoxia_3wks	-0.144	0.159
hypoxia_6wks	-0.205	0.125
glycerol	0.878	0.696
cholesterol	0.406	0.55
AJ	0.457	0.881
Bibs02	-0.015	0.587
Bibs02c	-0.033	0.033
BL6	-0.438	-0.222
BL6a	-0.29	-0.24
BXD01	0.13	0.197
BXD010	-0.299	-0.887
BXD011	-0.01	-0.66
BXD03	0.183	0.107
BXD04	-0.216	0.152
BXD05	0.309	-0.56
BXD06	-0.124	-0.555
BXD07	-0.057	-0.329
BXD08	0.152	-0.137
BXD09	-0.299	-0.145
CAST	0.279	0.507
CCcont	-0.379	-0.416
DS01	1.027	1.15
DS02	0.61	0.449
DS04	0.904	1.275
DS0c	1.193	0.448
GP01	-0.906	-0.411
GP02	0.944	-0.525
GP0c	-0.984	-0.573
NOD	-0.308	0.21
NZO	0.535	0.0
PWK	0.689	0.483
H37Rv_KO_CtpC	-0.804	-0.798
H37Rv_KO_CtpD	-1.941	-2.012
H37Rv_KO_Rv1272	0.109	0.519
H37Rv_KO_SugABC	-0.325	-0.084
H37Rv_KO_MbtN	-0.907	-0.781
Trans05	0.292	-0.905
macrophage_unactivated	0.679	0.537
IL1	0.383	0.504
Rapamycin	0.147	0.988
Tcell	-0.459	0.759
GMCSF	0.28	0.095
IFNab	0.036	-0.112
IFNg	-0.235	0.187
IFNg_GMCSF1	0.151	1.191
Rv1432_day32	0.738	-0.598
Rv1565c_day32	-0.3	0.0
secA2_input	0.715	0.866
delta_Rv3594	0.142	0.728
delta_Rv3717	0.117	0.482
delta_Rv3811	-0.274	0.091
delta_Rv0954	-0.578	1.031
PonA1	0.358	1.624
EccD1_KO	0.441	0.0
EspI_KO	0.168	1.081
PE35_KO	0.598	0.0
PPE68_KO	0.429	-0.358
glycerol2	0.158	0.087
lignocerate	0.138	-0.1
oleate	0.73	0.665
phosphatidylcholine	0.556	0.21
acetate	-0.1	-0.495
glucAc	-0.079	-0.646
Rv0950ko	0.425	-0.47
Rv1096ko	0.621	0.217
Rv3684ko	0.622	0.881
delta_otsA_trehalose	0.045	-0.512