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 Rv3518c/cyp142:

update plot	correlation	link to info on gene
Rv1525/wbbL2	(cc=0.545)	info on Rv1525/wbbL2
Rv3528c/-	(cc=0.4835)	info on Rv3528c/-
Rv0371c/-	(cc=0.4714)	info on Rv0371c/-
Rv1021/-	(cc=0.4629)	info on Rv1021/-
Rv0260c/-	(cc=0.4578)	info on Rv0260c/-
Rv0821c/phoY2	(cc=0.4417)	info on Rv0821c/phoY2
Rv3324c/moaC3	(cc=0.4367)	info on Rv3324c/moaC3
Rv0456B/mazE1	(cc=0.4345)	info on Rv0456B/mazE1
Rv3473c/bpoA	(cc=0.4344)	info on Rv3473c/bpoA
Rv1499/-	(cc=0.4279)	info on Rv1499/-

Correlation of Rv3518c/cyp142 with Rv1525/wbbL2

Normalized LFCs for Rv3518c/cyp142:
(description and provenance of datasets)

	Rv3518c/cyp142	Rv1525/wbbL2
Fe_supp_jason_reseq	1.241	0.587
low_pH_jason_reseq	-0.612	-0.303
NO_jason_reseq	-0.638	-1.32
B6_jason_reseq	0.368	-0.697
MHCII_jason_reseq	0.966	-0.492
Isoniazid02	-0.851	0.437
Rifampicin4	-0.1	0.428
Ethambutol3	-0.392	0.13
Meropenem3	-0.231	-0.068
Vancomycin16	0.096	0.419
Rv2680_day32	-0.065	-2.272
H37Rv_KO_MarP	0.549	0.706
hypoxia_3wks	-0.618	-0.167
hypoxia_6wks	0.493	-0.672
glycerol	0.12	0.0
cholesterol	0.119	0.178
AJ	-0.086	0.0
Bibs02	1.864	0.362
Bibs02c	1.172	1.516
BL6	1.405	1.322
BL6a	2.089	1.435
BXD01	0.52	0.433
BXD010	1.162	0.717
BXD011	0.399	1.699
BXD03	0.987	1.247
BXD04	1.283	0.923
BXD05	0.307	0.787
BXD06	0.776	0.996
BXD07	1.2	1.396
BXD08	1.293	0.905
BXD09	1.156	1.485
CAST	0.055	0.192
CCcont	1.187	1.377
DS01	-0.209	-0.45
DS02	0.454	-0.096
DS04	-0.146	-0.37
DS0c	-0.566	-1.065
GP01	-0.101	0.797
GP02	1.369	-0.353
GP0c	0.592	1.75
NOD	1.572	-0.205
NZO	0.355	0.0
PWK	-0.452	-0.087
H37Rv_KO_CtpC	0.039	0.824
H37Rv_KO_CtpD	-0.692	-0.918
H37Rv_KO_Rv1272	0.527	1.829
H37Rv_KO_SugABC	0.968	2.147
H37Rv_KO_MbtN	-0.285	-0.506
Trans05	0.477	0.393
macrophage_unactivated	0.114	0.628
IL1	1.13	0.792
Rapamycin	0.347	0.89
Tcell	0.45	0.573
GMCSF	0.557	-0.143
IFNab	0.082	0.671
IFNg	0.807	1.318
IFNg_GMCSF1	0.33	0.839
Rv1432_day32	0.0	0.061
Rv1565c_day32	0.952	-1.085
secA2_input	0.739	-1.431
delta_Rv3594	-1.101	-1.53
delta_Rv3717	-0.522	-1.608
delta_Rv3811	0.54	-1.774
delta_Rv0954	-0.93	-2.323
PonA1	0.223	-1.526
EccD1_KO	-0.204	-1.154
EspI_KO	-0.088	-0.471
PE35_KO	0.131	1.097
PPE68_KO	-0.301	1.104
glycerol2	0.446	0.581
lignocerate	1.119	1.29
oleate	-1.083	-1.596
phosphatidylcholine	0.716	0.762
acetate	1.232	1.76
glucAc	0.939	1.367
Rv0950ko	-0.051	-0.199
Rv1096ko	0.051	0.371
Rv3684ko	-0.056	0.593
delta_otsA_trehalose	-0.457	-0.075