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 Rv3142c/-

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

	Rv3517/-	Rv3142c/-
Fe_supp_jason_reseq	0.3	-0.278
low_pH_jason_reseq	-1.491	-0.852
NO_jason_reseq	-0.541	0.399
B6_jason_reseq	-0.856	-0.254
MHCII_jason_reseq	-0.266	-0.69
Isoniazid02	-0.419	-0.172
Rifampicin4	0.65	0.317
Ethambutol3	0.514	0.116
Meropenem3	1.004	0.019
Vancomycin16	-0.297	0.26
Rv2680_day32	-0.576	-0.971
H37Rv_KO_MarP	0.016	-0.155
hypoxia_3wks	-0.427	0.024
hypoxia_6wks	-0.397	-0.432
glycerol	-0.793	-0.825
cholesterol	0.252	0.155
AJ	1.592	1.219
Bibs02	0.736	0.257
Bibs02c	0.202	1.422
BL6	0.556	0.821
BL6a	-0.076	1.653
BXD01	0.731	0.919
BXD010	0.671	1.183
BXD011	0.3	1.105
BXD03	0.891	0.324
BXD04	0.279	0.606
BXD05	0.234	1.049
BXD06	0.218	0.946
BXD07	0.084	1.398
BXD08	1.061	0.626
BXD09	0.589	0.913
CAST	0.14	1.303
CCcont	0.639	0.784
DS01	0.869	0.79
DS02	0.354	0.521
DS04	1.117	0.512
DS0c	0.08	0.793
GP01	0.805	0.674
GP02	-0.124	0.388
GP0c	1.021	0.362
NOD	1.778	1.084
NZO	0.803	0.64
PWK	1.833	1.186
H37Rv_KO_CtpC	1.432	1.517
H37Rv_KO_CtpD	0.683	1.639
H37Rv_KO_Rv1272	1.625	1.18
H37Rv_KO_SugABC	0.39	1.178
H37Rv_KO_MbtN	-0.153	1.207
Trans05	1.08	1.301
macrophage_unactivated	0.698	0.104
IL1	0.036	-0.872
Rapamycin	-0.629	-0.353
Tcell	0.948	-0.186
GMCSF	0.063	-0.655
IFNab	0.245	-0.871
IFNg	-0.265	0.326
IFNg_GMCSF1	0.327	-0.088
Rv1432_day32	-0.394	-0.061
Rv1565c_day32	-0.357	0.204
secA2_input	0.332	0.059
delta_Rv3594	-0.408	-0.268
delta_Rv3717	-0.258	-0.294
delta_Rv3811	0.016	0.092
delta_Rv0954	-0.362	-0.322
PonA1	1.154	0.167
EccD1_KO	0.766	-0.342
EspI_KO	-0.439	0.211
PE35_KO	0.055	0.3
PPE68_KO	0.358	0.218
glycerol2	0.611	-0.092
lignocerate	0.746	0.754
oleate	0.956	-0.411
phosphatidylcholine	0.728	-0.022
acetate	0.12	0.213
glucAc	0.223	0.495
Rv0950ko	0.036	1.462
Rv1096ko	1.616	0.072
Rv3684ko	1.33	0.229
delta_otsA_trehalose	0.831	0.14