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 Rv0959/-

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

	Rv2860c/glnA4	Rv0959/-
Fe_supp_jason_reseq	0.272	0.791
low_pH_jason_reseq	0.348	0.132
NO_jason_reseq	-0.163	-0.454
B6_jason_reseq	1.016	0.968
MHCII_jason_reseq	1.38	1.232
Isoniazid02	0.528	0.439
Rifampicin4	-0.206	0.309
Ethambutol3	2.104	2.998
Meropenem3	0.435	0.491
Vancomycin16	0.443	0.255
Rv2680_day32	0.795	1.803
H37Rv_KO_MarP	-0.167	-0.037
hypoxia_3wks	-0.144	-0.072
hypoxia_6wks	-0.205	0.038
glycerol	0.878	0.786
cholesterol	0.406	0.706
AJ	0.457	-0.536
Bibs02	-0.015	0.51
Bibs02c	-0.033	-0.459
BL6	-0.438	-0.123
BL6a	-0.29	-0.601
BXD01	0.13	-0.379
BXD010	-0.299	-1.209
BXD011	-0.01	-1.144
BXD03	0.183	-1.156
BXD04	-0.216	-0.932
BXD05	0.309	-0.052
BXD06	-0.124	-0.663
BXD07	-0.057	-0.511
BXD08	0.152	-0.201
BXD09	-0.299	-0.808
CAST	0.279	-0.4
CCcont	-0.379	-0.571
DS01	1.027	0.065
DS02	0.61	0.759
DS04	0.904	-0.018
DS0c	1.193	0.41
GP01	-0.906	-0.476
GP02	0.944	0.805
GP0c	-0.984	-0.212
NOD	-0.308	0.241
NZO	0.535	-0.038
PWK	0.689	-0.453
H37Rv_KO_CtpC	-0.804	-1.32
H37Rv_KO_CtpD	-1.941	-0.954
H37Rv_KO_Rv1272	0.109	-0.659
H37Rv_KO_SugABC	-0.325	-0.434
H37Rv_KO_MbtN	-0.907	-2.086
Trans05	0.292	-0.482
macrophage_unactivated	0.679	1.872
IL1	0.383	0.068
Rapamycin	0.147	0.138
Tcell	-0.459	1.408
GMCSF	0.28	0.119
IFNab	0.036	-0.36
IFNg	-0.235	-1.384
IFNg_GMCSF1	0.151	-0.299
Rv1432_day32	0.738	0.754
Rv1565c_day32	-0.3	-0.37
secA2_input	0.715	-1.05
delta_Rv3594	0.142	-0.592
delta_Rv3717	0.117	-0.71
delta_Rv3811	-0.274	-0.983
delta_Rv0954	-0.578	-0.234
PonA1	0.358	0.072
EccD1_KO	0.441	0.0
EspI_KO	0.168	1.204
PE35_KO	0.598	0.971
PPE68_KO	0.429	1.283
glycerol2	0.158	0.053
lignocerate	0.138	0.069
oleate	0.73	0.328
phosphatidylcholine	0.556	0.52
acetate	-0.1	0.095
glucAc	-0.079	0.701
Rv0950ko	0.425	0.703
Rv1096ko	0.621	0.956
Rv3684ko	0.622	0.969
delta_otsA_trehalose	0.045	1.045