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 Rv1499/-

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

	Rv3518c/cyp142	Rv1499/-
Fe_supp_jason_reseq	1.241	1.255
low_pH_jason_reseq	-0.612	-0.432
NO_jason_reseq	-0.638	-0.903
B6_jason_reseq	0.368	0.09
MHCII_jason_reseq	0.966	-0.138
Isoniazid02	-0.851	-0.375
Rifampicin4	-0.1	-0.536
Ethambutol3	-0.392	-0.331
Meropenem3	-0.231	-0.339
Vancomycin16	0.096	-0.196
Rv2680_day32	-0.065	0.175
H37Rv_KO_MarP	0.549	-0.526
hypoxia_3wks	-0.618	-0.12
hypoxia_6wks	0.493	0.574
glycerol	0.12	-1.131
cholesterol	0.119	-0.38
AJ	-0.086	0.024
Bibs02	1.864	0.574
Bibs02c	1.172	0.258
BL6	1.405	0.806
BL6a	2.089	-0.225
BXD01	0.52	0.515
BXD010	1.162	0.021
BXD011	0.399	0.388
BXD03	0.987	1.053
BXD04	1.283	0.749
BXD05	0.307	0.33
BXD06	0.776	0.402
BXD07	1.2	0.579
BXD08	1.293	0.927
BXD09	1.156	0.752
CAST	0.055	0.325
CCcont	1.187	1.221
DS01	-0.209	0.086
DS02	0.454	0.036
DS04	-0.146	-0.797
DS0c	-0.566	0.357
GP01	-0.101	-0.725
GP02	1.369	0.852
GP0c	0.592	-0.44
NOD	1.572	-0.298
NZO	0.355	0.952
PWK	-0.452	-0.074
H37Rv_KO_CtpC	0.039	0.984
H37Rv_KO_CtpD	-0.692	1.16
H37Rv_KO_Rv1272	0.527	0.512
H37Rv_KO_SugABC	0.968	0.481
H37Rv_KO_MbtN	-0.285	0.679
Trans05	0.477	0.207
macrophage_unactivated	0.114	2.838
IL1	1.13	0.638
Rapamycin	0.347	-0.212
Tcell	0.45	1.14
GMCSF	0.557	0.908
IFNab	0.082	0.154
IFNg	0.807	0.556
IFNg_GMCSF1	0.33	0.892
Rv1432_day32	0.0	0.231
Rv1565c_day32	0.952	0.584
secA2_input	0.739	-0.061
delta_Rv3594	-1.101	-0.286
delta_Rv3717	-0.522	-0.909
delta_Rv3811	0.54	-0.149
delta_Rv0954	-0.93	-0.423
PonA1	0.223	-0.616
EccD1_KO	-0.204	-0.329
EspI_KO	-0.088	-0.471
PE35_KO	0.131	-0.239
PPE68_KO	-0.301	0.211
glycerol2	0.446	1.606
lignocerate	1.119	2.356
oleate	-1.083	-0.872
phosphatidylcholine	0.716	1.756
acetate	1.232	1.081
glucAc	0.939	1.473
Rv0950ko	-0.051	0.817
Rv1096ko	0.051	-0.308
Rv3684ko	-0.056	-0.334
delta_otsA_trehalose	-0.457	0.256