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 Rv2497c/bkdA:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.5361)	info on Rv3738c/PPE66
Rv0742/PE_PGRS8	(cc=0.5068)	info on Rv0742/PE_PGRS8
Rv2871/vapB43	(cc=0.4892)	info on Rv2871/vapB43
Rv3694c/-	(cc=0.4833)	info on Rv3694c/-
Rv3688c/-	(cc=0.4766)	info on Rv3688c/-
Rv1498c/-	(cc=0.4603)	info on Rv1498c/-
Rv2300c/-	(cc=0.4583)	info on Rv2300c/-
Rv1809/PPE33	(cc=0.456)	info on Rv1809/PPE33
Rv0397A/-	(cc=0.453)	info on Rv0397A/-
Rv2947c/pks15	(cc=0.4452)	info on Rv2947c/pks15

Correlation of Rv2497c/bkdA with Rv3694c/-

Normalized LFCs for Rv2497c/bkdA:
(description and provenance of datasets)

	Rv2497c/bkdA	Rv3694c/-
Fe_supp_jason_reseq	-0.297	0.032
low_pH_jason_reseq	0.244	-2.168
NO_jason_reseq	0.36	-0.948
B6_jason_reseq	-1.575	-1.304
MHCII_jason_reseq	0.011	-2.269
Isoniazid02	-1.077	-0.37
Rifampicin4	0.263	-0.999
Ethambutol3	-1.058	-0.179
Meropenem3	-0.461	-0.115
Vancomycin16	-1.035	0.297
Rv2680_day32	-0.473	0.339
H37Rv_KO_MarP	-0.144	-0.586
hypoxia_3wks	0.634	0.275
hypoxia_6wks	-0.578	0.708
glycerol	-1.842	-1.539
cholesterol	0.311	-0.233
AJ	-0.062	1.23
Bibs02	0.432	-0.691
Bibs02c	0.426	0.152
BL6	0.255	1.824
BL6a	0.666	0.864
BXD01	0.147	1.257
BXD010	0.491	0.693
BXD011	0.476	1.576
BXD03	-0.389	1.065
BXD04	-0.334	0.896
BXD05	0.528	0.911
BXD06	0.342	1.028
BXD07	0.641	1.463
BXD08	0.118	1.264
BXD09	0.732	0.909
CAST	-1.006	-0.132
CCcont	0.444	1.589
DS01	0.238	-0.089
DS02	-0.375	-0.399
DS04	0.125	0.748
DS0c	0.644	-1.131
GP01	0.682	0.795
GP02	0.178	0.074
GP0c	0.192	0.614
NOD	-0.218	-0.973
NZO	0.103	0.525
PWK	0.503	2.1
H37Rv_KO_CtpC	1.407	1.972
H37Rv_KO_CtpD	0.299	0.135
H37Rv_KO_Rv1272	1.469	2.263
H37Rv_KO_SugABC	1.395	1.67
H37Rv_KO_MbtN	0.21	0.932
Trans05	0.92	2.032
macrophage_unactivated	1.111	0.505
IL1	0.676	0.362
Rapamycin	0.246	-0.408
Tcell	0.668	0.802
GMCSF	0.784	0.65
IFNab	0.828	0.992
IFNg	1.053	0.965
IFNg_GMCSF1	0.49	0.735
Rv1432_day32	-0.117	0.424
Rv1565c_day32	-0.542	-0.937
secA2_input	0.509	-0.562
delta_Rv3594	-0.24	-1.023
delta_Rv3717	0.305	-0.351
delta_Rv3811	-0.214	0.416
delta_Rv0954	-0.669	-0.39
PonA1	-0.777	-0.706
EccD1_KO	-0.51	-0.625
EspI_KO	-1.072	0.088
PE35_KO	0.184	0.149
PPE68_KO	0.422	0.131
glycerol2	0.581	0.045
lignocerate	1.132	-0.06
oleate	1.466	0.836
phosphatidylcholine	0.753	-0.19
acetate	0.775	0.464
glucAc	0.0	0.288
Rv0950ko	-0.172	-0.244
Rv1096ko	0.066	0.558
Rv3684ko	0.0	0.91
delta_otsA_trehalose	-0.184	0.385