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 Rv0549c/vapC3:

update plot	correlation	link to info on gene
Rv1314c/-	(cc=0.4455)	info on Rv1314c/-
Rv3497c/mce4C	(cc=0.4166)	info on Rv3497c/mce4C
Rv2261c/-	(cc=0.4099)	info on Rv2261c/-
Rv3496c/mce4D	(cc=0.402)	info on Rv3496c/mce4D
Rv1492/mutA	(cc=0.399)	info on Rv1492/mutA
Rv2855/mtr	(cc=0.3922)	info on Rv2855/mtr
Rv1569/bioF1	(cc=0.3871)	info on Rv1569/bioF1
Rv3501c/yrbE4A	(cc=0.3816)	info on Rv3501c/yrbE4A
Rv1259/udgB	(cc=0.3792)	info on Rv1259/udgB
Rv3492c/-	(cc=0.3778)	info on Rv3492c/-

Correlation of Rv0549c/vapC3 with Rv1259/udgB

Normalized LFCs for Rv0549c/vapC3:
(description and provenance of datasets)

	Rv0549c/vapC3	Rv1259/udgB
Fe_supp_jason_reseq	2.234	-0.232
low_pH_jason_reseq	0.201	1.106
NO_jason_reseq	0.226	-0.74
B6_jason_reseq	-0.805	-1.01
MHCII_jason_reseq	1.217	0.109
Isoniazid02	0.455	0.377
Rifampicin4	0.677	0.203
Ethambutol3	1.021	0.15
Meropenem3	0.072	2.731
Vancomycin16	0.597	0.799
Rv2680_day32	-0.305	0.811
H37Rv_KO_MarP	0.569	-0.512
hypoxia_3wks	0.614	-0.786
hypoxia_6wks	-0.501	-0.217
glycerol	0.162	0.992
cholesterol	-0.631	0.58
AJ	-1.788	-0.541
Bibs02	-2.853	-1.976
Bibs02c	1.585	1.258
BL6	1.041	2.816
BL6a	1.012	1.435
BXD01	0.276	1.192
BXD010	0.318	0.513
BXD011	-0.415	1.585
BXD03	0.594	0.258
BXD04	-0.098	0.283
BXD05	-0.915	0.792
BXD06	0.619	1.787
BXD07	0.587	1.226
BXD08	1.437	0.867
BXD09	0.77	1.143
CAST	-1.138	-0.821
CCcont	0.61	0.598
DS01	-0.948	0.496
DS02	-1.24	0.457
DS04	0.299	0.294
DS0c	-0.28	0.456
GP01	0.433	0.824
GP02	1.789	1.275
GP0c	-0.091	0.865
NOD	-1.31	-1.113
NZO	-2.159	-0.646
PWK	0.158	-0.574
H37Rv_KO_CtpC	0.304	0.774
H37Rv_KO_CtpD	-2.21	-0.451
H37Rv_KO_Rv1272	0.432	-0.413
H37Rv_KO_SugABC	-0.254	-0.695
H37Rv_KO_MbtN	-1.051	0.923
Trans05	1.153	0.661
macrophage_unactivated	0.366	0.0
IL1	0.148	1.898
Rapamycin	0.525	0.727
Tcell	0.815	1.652
GMCSF	0.106	-0.206
IFNab	-0.45	-1.932
IFNg	-0.11	-0.294
IFNg_GMCSF1	-1.854	-0.503
Rv1432_day32	0.804	-0.85
Rv1565c_day32	-0.456	-0.218
secA2_input	1.295	-0.083
delta_Rv3594	1.031	0.84
delta_Rv3717	1.399	0.534
delta_Rv3811	-0.775	0.706
delta_Rv0954	0.279	0.859
PonA1	0.335	0.297
EccD1_KO	1.197	0.174
EspI_KO	0.667	0.077
PE35_KO	1.269	0.726
PPE68_KO	0.71	0.253
glycerol2	-0.121	0.722
lignocerate	0.651	0.289
oleate	0.569	0.437
phosphatidylcholine	0.377	0.803
acetate	0.725	-0.336
glucAc	0.028	-0.773
Rv0950ko	-0.663	1.251
Rv1096ko	0.642	-0.247
Rv3684ko	1.585	0.652
delta_otsA_trehalose	0.623	0.472