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 Rv3517/-:

update plot	correlation	link to info on gene
Rv3694c/-	(cc=0.4981)	info on Rv3694c/-
Rv3689/-	(cc=0.4812)	info on Rv3689/-
Rv3796/-	(cc=0.4794)	info on Rv3796/-
Rv2253/-	(cc=0.4682)	info on Rv2253/-
Rv0831c/-	(cc=0.463)	info on Rv0831c/-
Rv3744/nmtR	(cc=0.4522)	info on Rv3744/nmtR
Rv3695/-	(cc=0.4453)	info on Rv3695/-
Rv1585c/-	(cc=0.4422)	info on Rv1585c/-
Rv3142c/-	(cc=0.4388)	info on Rv3142c/-
Rv3378c/-	(cc=0.4266)	info on Rv3378c/-

Correlation of Rv3517/- with Rv2253/-

Normalized LFCs for Rv3517/-:
(description and provenance of datasets)

	Rv3517/-	Rv2253/-
Fe_supp_jason_reseq	0.3	-1.163
low_pH_jason_reseq	-1.491	-0.206
NO_jason_reseq	-0.541	-0.475
B6_jason_reseq	-0.856	-2.027
MHCII_jason_reseq	-0.266	-1.199
Isoniazid02	-0.419	-0.095
Rifampicin4	0.65	-0.845
Ethambutol3	0.514	-0.304
Meropenem3	1.004	-0.432
Vancomycin16	-0.297	-0.172
Rv2680_day32	-0.576	0.456
H37Rv_KO_MarP	0.016	-0.167
hypoxia_3wks	-0.427	0.167
hypoxia_6wks	-0.397	-0.867
glycerol	-0.793	-0.903
cholesterol	0.252	-0.807
AJ	1.592	1.758
Bibs02	0.736	0.719
Bibs02c	0.202	-0.418
BL6	0.556	0.656
BL6a	-0.076	-0.626
BXD01	0.731	1.271
BXD010	0.671	0.707
BXD011	0.3	0.54
BXD03	0.891	0.327
BXD04	0.279	0.407
BXD05	0.234	0.301
BXD06	0.218	0.483
BXD07	0.084	0.259
BXD08	1.061	1.186
BXD09	0.589	0.462
CAST	0.14	0.102
CCcont	0.639	1.443
DS01	0.869	0.395
DS02	0.354	-0.495
DS04	1.117	1.269
DS0c	0.08	-0.823
GP01	0.805	-0.119
GP02	-0.124	-0.603
GP0c	1.021	-0.333
NOD	1.778	2.791
NZO	0.803	1.305
PWK	1.833	-0.287
H37Rv_KO_CtpC	1.432	1.54
H37Rv_KO_CtpD	0.683	1.877
H37Rv_KO_Rv1272	1.625	1.952
H37Rv_KO_SugABC	0.39	1.701
H37Rv_KO_MbtN	-0.153	0.452
Trans05	1.08	2.427
macrophage_unactivated	0.698	0.915
IL1	0.036	-1.077
Rapamycin	-0.629	-2.829
Tcell	0.948	1.049
GMCSF	0.063	-2.857
IFNab	0.245	-0.943
IFNg	-0.265	-0.703
IFNg_GMCSF1	0.327	-1.141
Rv1432_day32	-0.394	1.096
Rv1565c_day32	-0.357	0.141
secA2_input	0.332	-0.366
delta_Rv3594	-0.408	0.445
delta_Rv3717	-0.258	-0.505
delta_Rv3811	0.016	-0.152
delta_Rv0954	-0.362	-0.668
PonA1	1.154	-0.32
EccD1_KO	0.766	-0.125
EspI_KO	-0.439	0.502
PE35_KO	0.055	0.417
PPE68_KO	0.358	-0.246
glycerol2	0.611	1.26
lignocerate	0.746	1.393
oleate	0.956	0.664
phosphatidylcholine	0.728	1.259
acetate	0.12	1.413
glucAc	0.223	0.939
Rv0950ko	0.036	-0.576
Rv1096ko	1.616	-1.007
Rv3684ko	1.33	-0.626
delta_otsA_trehalose	0.831	-0.026