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 Rv3394c/-:

update plot	correlation	link to info on gene
Rv3511/PE_PGRS55	(cc=0.5008)	info on Rv3511/PE_PGRS55
Rv3514/PE_PGRS57	(cc=0.4562)	info on Rv3514/PE_PGRS57
Rv3508/PE_PGRS54	(cc=0.4517)	info on Rv3508/PE_PGRS54
Rv2853/PE_PGRS48	(cc=0.4274)	info on Rv2853/PE_PGRS48
Rv2431c/PE25	(cc=0.405)	info on Rv2431c/PE25
Rv0834c/PE_PGRS14	(cc=0.4013)	info on Rv0834c/PE_PGRS14
Rv0142/-	(cc=0.3995)	info on Rv0142/-
Rv3299c/atsB	(cc=0.399)	info on Rv3299c/atsB
Rv0858c/dapC	(cc=0.3974)	info on Rv0858c/dapC
Rv3470c/ilvB2	(cc=0.3907)	info on Rv3470c/ilvB2

Correlation of Rv3394c/- with Rv3511/PE_PGRS55

Normalized LFCs for Rv3394c/-:
(description and provenance of datasets)

	Rv3394c/-	Rv3511/PE_PGRS55
Fe_supp_jason_reseq	-0.829	-0.718
low_pH_jason_reseq	1.228	-0.269
NO_jason_reseq	0.591	-0.278
B6_jason_reseq	-1.269	-0.682
MHCII_jason_reseq	-0.58	0.111
Isoniazid02	-0.339	-1.059
Rifampicin4	0.72	0.444
Ethambutol3	-0.197	-0.565
Meropenem3	0.207	-0.213
Vancomycin16	0.0	-0.348
Rv2680_day32	-0.422	-0.922
H37Rv_KO_MarP	0.289	0.014
hypoxia_3wks	0.439	-0.618
hypoxia_6wks	-0.048	-1.347
glycerol	2.058	0.686
cholesterol	1.696	0.429
AJ	1.627	0.844
Bibs02	0.0	-0.334
Bibs02c	0.756	0.685
BL6	0.16	-0.228
BL6a	0.443	0.321
BXD01	0.029	0.31
BXD010	0.4	-0.196
BXD011	0.137	-0.297
BXD03	0.399	1.067
BXD04	0.486	0.287
BXD05	0.373	0.589
BXD06	0.417	0.178
BXD07	0.232	0.41
BXD08	1.2	0.632
BXD09	0.39	0.287
CAST	0.385	0.075
CCcont	0.677	-0.025
DS01	0.777	-0.866
DS02	0.364	-0.112
DS04	1.147	-0.083
DS0c	-0.823	-0.484
GP01	1.305	0.579
GP02	1.89	1.313
GP0c	0.769	0.699
NOD	-0.158	-0.322
NZO	0.446	1.052
PWK	0.0	0.374
H37Rv_KO_CtpC	0.587	0.561
H37Rv_KO_CtpD	0.351	0.302
H37Rv_KO_Rv1272	1.115	0.058
H37Rv_KO_SugABC	0.659	0.649
H37Rv_KO_MbtN	-0.024	0.319
Trans05	1.567	1.249
macrophage_unactivated	-0.114	0.073
IL1	0.727	-0.59
Rapamycin	-0.055	-0.611
Tcell	-0.554	-0.479
GMCSF	0.317	0.544
IFNab	-0.109	-0.683
IFNg	0.406	-0.497
IFNg_GMCSF1	1.09	-0.421
Rv1432_day32	1.112	1.036
Rv1565c_day32	1.887	-0.524
secA2_input	0.269	0.446
delta_Rv3594	-0.078	-0.135
delta_Rv3717	0.062	-0.53
delta_Rv3811	0.073	-0.349
delta_Rv0954	0.124	-0.808
PonA1	0.329	0.0
EccD1_KO	0.753	0.444
EspI_KO	-0.322	-0.225
PE35_KO	-0.137	-0.63
PPE68_KO	0.099	-0.733
glycerol2	-0.059	0.248
lignocerate	0.499	0.342
oleate	0.274	0.166
phosphatidylcholine	0.296	0.221
acetate	0.733	-0.057
glucAc	0.307	-0.023
Rv0950ko	0.1	0.609
Rv1096ko	0.473	0.531
Rv3684ko	1.52	-0.193
delta_otsA_trehalose	-0.045	-1.443