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 Rv3224B/-:

update plot	correlation	link to info on gene
Rv3224A/-	(cc=0.5299)	info on Rv3224A/-
Rv3335c/-	(cc=0.522)	info on Rv3335c/-
Rv2077A/-	(cc=0.5179)	info on Rv2077A/-
Rv0060/-	(cc=0.5046)	info on Rv0060/-
Rv3819/-	(cc=0.4792)	info on Rv3819/-
Rv3127/-	(cc=0.4743)	info on Rv3127/-
Rv2821c/-	(cc=0.473)	info on Rv2821c/-
Rv0312/-	(cc=0.4683)	info on Rv0312/-
Rv0042c/-	(cc=0.4667)	info on Rv0042c/-
Rv1987/-	(cc=0.4655)	info on Rv1987/-

Correlation of Rv3224B/- with Rv3127/-

Normalized LFCs for Rv3224B/-:
(description and provenance of datasets)

	Rv3224B/-	Rv3127/-
Fe_supp_jason_reseq	1.613	0.524
low_pH_jason_reseq	0.582	0.555
NO_jason_reseq	1.003	0.767
B6_jason_reseq	1.336	-0.517
MHCII_jason_reseq	-0.043	0.203
Isoniazid02	0.0	-0.194
Rifampicin4	0.43	0.485
Ethambutol3	-0.204	1.054
Meropenem3	2.432	2.889
Vancomycin16	-0.202	0.573
Rv2680_day32	1.574	0.383
H37Rv_KO_MarP	-0.34	1.082
hypoxia_3wks	-1.798	-0.694
hypoxia_6wks	-0.764	0.727
glycerol	-1.318	-1.009
cholesterol	-0.644	-0.338
AJ	0.338	-0.424
Bibs02	1.041	-1.658
Bibs02c	0.32	-0.908
BL6	2.331	1.453
BL6a	0.016	-1.201
BXD01	0.306	0.552
BXD010	-0.741	0.678
BXD011	-0.167	0.575
BXD03	0.361	-0.149
BXD04	0.999	0.214
BXD05	-0.022	-0.423
BXD06	-0.239	-0.277
BXD07	0.12	-0.287
BXD08	0.422	-0.177
BXD09	-0.917	-0.656
CAST	0.384	-0.791
CCcont	0.0	0.772
DS01	-0.905	0.722
DS02	0.156	0.525
DS04	-1.487	-0.169
DS0c	-1.483	0.698
GP01	0.393	-0.801
GP02	-1.146	0.637
GP0c	0.18	0.721
NOD	-0.037	-0.195
NZO	0.829	-0.173
PWK	-0.134	0.232
H37Rv_KO_CtpC	-1.011	0.192
H37Rv_KO_CtpD	2.225	0.387
H37Rv_KO_Rv1272	-1.207	1.464
H37Rv_KO_SugABC	-0.776	-0.529
H37Rv_KO_MbtN	0.961	0.621
Trans05	0.957	1.161
macrophage_unactivated	1.285	0.776
IL1	-1.99	-0.308
Rapamycin	-0.546	-0.666
Tcell	1.942	0.417
GMCSF	-0.784	-0.372
IFNab	-0.426	-0.209
IFNg	0.583	-0.684
IFNg_GMCSF1	-1.2	-0.933
Rv1432_day32	0.321	0.939
Rv1565c_day32	-1.093	0.553
secA2_input	0.167	-0.418
delta_Rv3594	0.382	-0.332
delta_Rv3717	-1.565	-0.206
delta_Rv3811	1.008	0.239
delta_Rv0954	0.27	-0.584
PonA1	-0.851	-1.829
EccD1_KO	-1.092	-0.865
EspI_KO	-2.738	-0.53
PE35_KO	-2.033	-0.064
PPE68_KO	-0.749	0.138
glycerol2	2.191	1.545
lignocerate	2.565	2.115
oleate	-1.167	-0.614
phosphatidylcholine	2.333	1.437
acetate	3.501	1.278
glucAc	2.476	1.483
Rv0950ko	0.112	-0.338
Rv1096ko	0.531	-0.19
Rv3684ko	0.062	-0.589
delta_otsA_trehalose	-0.835	0.36