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 Rv2352c/PPE38:

update plot	correlation	link to info on gene
Rv0160c/PE4	(cc=0.5845)	info on Rv0160c/PE4
Rv3161c/-	(cc=0.5722)	info on Rv3161c/-
Rv0354c/PPE7	(cc=0.5707)	info on Rv0354c/PPE7
Rv1504c/-	(cc=0.5614)	info on Rv1504c/-
Rv2947c/pks15	(cc=0.5506)	info on Rv2947c/pks15
Rv1278/-	(cc=0.5437)	info on Rv1278/-
Rv3919c/gid	(cc=0.5421)	info on Rv3919c/gid
Rv0073/-	(cc=0.5416)	info on Rv0073/-
Rv0469/umaA	(cc=0.5381)	info on Rv0469/umaA
Rv2853/PE_PGRS48	(cc=0.5372)	info on Rv2853/PE_PGRS48

Correlation of Rv2352c/PPE38 with Rv0469/umaA

Normalized LFCs for Rv2352c/PPE38:
(description and provenance of datasets)

	Rv2352c/PPE38	Rv0469/umaA
Fe_supp_jason_reseq	0.35	1.002
low_pH_jason_reseq	-1.029	0.125
NO_jason_reseq	-0.491	0.039
B6_jason_reseq	-0.488	-0.616
MHCII_jason_reseq	-0.46	-0.862
Isoniazid02	-1.043	-0.34
Rifampicin4	-0.208	-0.558
Ethambutol3	-0.882	0.193
Meropenem3	-1.085	0.291
Vancomycin16	-0.602	-0.403
Rv2680_day32	-0.611	-1.846
H37Rv_KO_MarP	-0.629	0.119
hypoxia_3wks	-0.06	0.12
hypoxia_6wks	-0.56	0.157
glycerol	0.532	0.565
cholesterol	0.575	0.048
AJ	0.321	0.397
Bibs02	0.203	-0.411
Bibs02c	0.297	0.297
BL6	0.173	-0.021
BL6a	0.425	1.129
BXD01	0.346	0.624
BXD010	-0.031	1.099
BXD011	-0.232	0.879
BXD03	0.503	0.588
BXD04	0.661	1.348
BXD05	0.358	0.997
BXD06	0.167	0.761
BXD07	0.22	0.856
BXD08	0.298	0.705
BXD09	0.376	0.815
CAST	0.235	0.292
CCcont	-0.032	0.379
DS01	0.267	-0.482
DS02	0.17	0.744
DS04	0.554	0.663
DS0c	0.179	-0.355
GP01	0.253	1.709
GP02	0.349	0.189
GP0c	0.348	0.803
NOD	-0.184	-0.197
NZO	0.393	0.425
PWK	0.06	0.718
H37Rv_KO_CtpC	0.169	0.812
H37Rv_KO_CtpD	0.659	1.551
H37Rv_KO_Rv1272	1.248	2.299
H37Rv_KO_SugABC	0.005	1.213
H37Rv_KO_MbtN	0.457	0.693
Trans05	1.088	1.456
macrophage_unactivated	0.511	0.426
IL1	-0.11	-0.258
Rapamycin	0.037	-0.457
Tcell	-0.495	0.44
GMCSF	0.533	0.288
IFNab	0.054	0.127
IFNg	0.088	0.361
IFNg_GMCSF1	0.364	0.465
Rv1432_day32	0.407	0.162
Rv1565c_day32	-0.141	-0.027
secA2_input	-0.626	-1.124
delta_Rv3594	0.583	0.75
delta_Rv3717	-0.374	0.367
delta_Rv3811	0.268	0.568
delta_Rv0954	0.289	0.18
PonA1	0.085	1.236
EccD1_KO	-0.566	-0.339
EspI_KO	-0.031	-0.756
PE35_KO	0.105	-1.178
PPE68_KO	0.275	-0.806
glycerol2	0.167	-0.02
lignocerate	-0.169	-0.218
oleate	-0.004	0.461
phosphatidylcholine	-0.224	0.204
acetate	-0.047	-0.244
glucAc	0.016	-0.555
Rv0950ko	0.277	0.311
Rv1096ko	-0.012	-0.41
Rv3684ko	-0.134	-0.799
delta_otsA_trehalose	0.184	0.097