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 Rv3796/-:

update plot	correlation	link to info on gene
Rv1500/-	(cc=0.687)	info on Rv1500/-
Rv2430c/PPE41	(cc=0.6505)	info on Rv2430c/PPE41
Rv3142c/-	(cc=0.6429)	info on Rv3142c/-
Rv0469/umaA	(cc=0.6316)	info on Rv0469/umaA
Rv2735c/-	(cc=0.6085)	info on Rv2735c/-
Rv1918c/PPE35	(cc=0.5988)	info on Rv1918c/PPE35
Rv0305c/PPE6	(cc=0.5975)	info on Rv0305c/PPE6
Rv1059/-	(cc=0.5901)	info on Rv1059/-
Rv3156/nuoL	(cc=0.5858)	info on Rv3156/nuoL
Rv0642c/mmaA4	(cc=0.5714)	info on Rv0642c/mmaA4

Correlation of Rv3796/- with Rv1500/-

Normalized LFCs for Rv3796/-:
(description and provenance of datasets)

	Rv3796/-	Rv1500/-
Fe_supp_jason_reseq	0.216	0.172
low_pH_jason_reseq	-0.253	-0.586
NO_jason_reseq	-0.063	-0.446
B6_jason_reseq	-0.018	-0.01
MHCII_jason_reseq	-0.072	0.098
Isoniazid02	-0.361	-0.473
Rifampicin4	0.623	-0.796
Ethambutol3	-0.165	-0.894
Meropenem3	0.966	0.685
Vancomycin16	0.085	-0.841
Rv2680_day32	-0.562	-0.08
H37Rv_KO_MarP	0.477	-0.391
hypoxia_3wks	0.0	-0.108
hypoxia_6wks	-0.198	0.234
glycerol	-0.48	-1.131
cholesterol	-0.036	-0.784
AJ	1.324	0.531
Bibs02	-0.091	0.385
Bibs02c	0.897	0.674
BL6	0.714	1.36
BL6a	1.187	1.39
BXD01	0.694	1.048
BXD010	0.944	1.108
BXD011	0.969	1.41
BXD03	0.803	0.918
BXD04	0.849	0.882
BXD05	1.394	1.222
BXD06	0.664	1.498
BXD07	0.75	1.011
BXD08	0.98	1.618
BXD09	0.971	1.389
CAST	0.552	1.059
CCcont	0.396	1.057
DS01	0.392	0.366
DS02	0.361	0.517
DS04	0.564	0.146
DS0c	0.811	0.919
GP01	1.283	1.618
GP02	0.027	0.833
GP0c	0.613	0.748
NOD	1.059	1.233
NZO	1.195	0.27
PWK	0.594	0.601
H37Rv_KO_CtpC	0.521	1.204
H37Rv_KO_CtpD	0.584	1.362
H37Rv_KO_Rv1272	1.414	1.369
H37Rv_KO_SugABC	0.936	1.232
H37Rv_KO_MbtN	0.828	0.936
Trans05	0.764	0.275
macrophage_unactivated	0.527	0.527
IL1	0.024	0.0
Rapamycin	0.295	0.184
Tcell	0.124	0.759
GMCSF	-0.04	0.217
IFNab	-0.045	0.024
IFNg	-0.104	0.315
IFNg_GMCSF1	0.189	0.327
Rv1432_day32	-0.269	0.289
Rv1565c_day32	0.374	0.757
secA2_input	0.302	-0.513
delta_Rv3594	0.211	-0.145
delta_Rv3717	0.356	-0.57
delta_Rv3811	0.104	-0.474
delta_Rv0954	0.746	0.09
PonA1	0.28	-0.269
EccD1_KO	-0.335	-0.263
EspI_KO	-0.73	-0.171
PE35_KO	-0.298	0.029
PPE68_KO	-0.352	0.061
glycerol2	0.235	0.748
lignocerate	0.078	0.804
oleate	0.586	0.57
phosphatidylcholine	0.246	0.969
acetate	-0.229	-0.12
glucAc	-0.347	-0.042
Rv0950ko	0.057	0.1
Rv1096ko	-0.115	-0.7
Rv3684ko	0.239	-0.308
delta_otsA_trehalose	-0.027	0.147