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 Rv1678/-:

update plot	correlation	link to info on gene
Rv0940c/-	(cc=0.5598)	info on Rv0940c/-
Rv2738c/-	(cc=0.5484)	info on Rv2738c/-
Rv2544/lppB	(cc=0.4987)	info on Rv2544/lppB
Rv2558/-	(cc=0.472)	info on Rv2558/-
Rv3473c/bpoA	(cc=0.4718)	info on Rv3473c/bpoA
Rv1167c/-	(cc=0.4715)	info on Rv1167c/-
Rv1903/-	(cc=0.4691)	info on Rv1903/-
Rv3045/adhC	(cc=0.468)	info on Rv3045/adhC
Rv3397c/phyA	(cc=0.4679)	info on Rv3397c/phyA
Rv0042c/-	(cc=0.465)	info on Rv0042c/-

Correlation of Rv1678/- with Rv2558/-

Normalized LFCs for Rv1678/-:
(description and provenance of datasets)

	Rv1678/-	Rv2558/-
Fe_supp_jason_reseq	-0.603	-0.021
low_pH_jason_reseq	2.096	0.815
NO_jason_reseq	-0.105	0.226
B6_jason_reseq	-2.073	-0.969
MHCII_jason_reseq	0.526	-0.241
Isoniazid02	-2.721	-2.203
Rifampicin4	1.032	-1.633
Ethambutol3	-2.157	-1.734
Meropenem3	-1.042	-1.416
Vancomycin16	-0.801	-1.73
Rv2680_day32	0.068	0.877
H37Rv_KO_MarP	-0.673	-0.066
hypoxia_3wks	-0.961	-0.574
hypoxia_6wks	0.497	-0.564
glycerol	1.333	0.197
cholesterol	0.264	-0.069
AJ	-0.585	0.217
Bibs02	1.974	-0.105
Bibs02c	-0.399	-0.764
BL6	0.859	-0.49
BL6a	1.69	0.26
BXD01	0.291	0.048
BXD010	0.912	0.933
BXD011	1.015	-0.269
BXD03	2.0	0.0
BXD04	1.013	0.227
BXD05	1.302	0.154
BXD06	0.543	-0.352
BXD07	1.34	0.27
BXD08	0.878	0.201
BXD09	1.303	-0.388
CAST	0.514	0.073
CCcont	1.385	0.393
DS01	1.465	-0.033
DS02	0.654	0.466
DS04	1.546	0.181
DS0c	-0.11	0.39
GP01	-0.077	0.777
GP02	-1.089	0.019
GP0c	0.573	1.058
NOD	0.264	0.778
NZO	0.279	0.724
PWK	-0.205	0.509
H37Rv_KO_CtpC	1.028	0.305
H37Rv_KO_CtpD	2.483	1.664
H37Rv_KO_Rv1272	0.501	-0.621
H37Rv_KO_SugABC	-1.066	0.347
H37Rv_KO_MbtN	2.197	0.57
Trans05	2.198	0.431
macrophage_unactivated	0.571	0.877
IL1	1.035	0.273
Rapamycin	0.436	0.199
Tcell	-0.104	-0.205
GMCSF	0.451	0.283
IFNab	1.206	0.463
IFNg	-0.235	-0.342
IFNg_GMCSF1	-0.496	0.575
Rv1432_day32	0.0	-0.445
Rv1565c_day32	2.098	-0.499
secA2_input	-0.042	0.695
delta_Rv3594	0.858	1.826
delta_Rv3717	1.452	0.552
delta_Rv3811	1.17	0.571
delta_Rv0954	1.47	1.689
PonA1	1.133	0.878
EccD1_KO	0.164	0.635
EspI_KO	0.787	-0.325
PE35_KO	0.618	0.502
PPE68_KO	1.014	-0.038
glycerol2	0.321	-0.705
lignocerate	2.26	-0.028
oleate	-1.983	-0.081
phosphatidylcholine	1.401	-0.436
acetate	2.522	0.878
glucAc	2.538	0.561
Rv0950ko	-0.935	-0.16
Rv1096ko	-0.766	-0.326
Rv3684ko	0.223	-1.932
delta_otsA_trehalose	-1.065	-0.347