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 Rv3301c/phoY1:

update plot	correlation	link to info on gene
Rv2623/TB31.7	(cc=0.5231)	info on Rv2623/TB31.7
Rv2813/-	(cc=0.51)	info on Rv2813/-
Rv2544/lppB	(cc=0.5047)	info on Rv2544/lppB
Rv2960c/-	(cc=0.5033)	info on Rv2960c/-
Rv1987/-	(cc=0.4721)	info on Rv1987/-
Rv3045/adhC	(cc=0.4665)	info on Rv3045/adhC
Rv3010c/pfkA	(cc=0.4648)	info on Rv3010c/pfkA
Rv3133c/devR	(cc=0.4559)	info on Rv3133c/devR
Rv0945/-	(cc=0.454)	info on Rv0945/-
Rv2276/cyp121	(cc=0.4518)	info on Rv2276/cyp121

Correlation of Rv3301c/phoY1 with Rv2813/-

Normalized LFCs for Rv3301c/phoY1:
(description and provenance of datasets)

	Rv3301c/phoY1	Rv2813/-
Fe_supp_jason_reseq	0.633	0.747
low_pH_jason_reseq	-0.515	-0.43
NO_jason_reseq	0.189	-1.735
B6_jason_reseq	-0.846	-0.733
MHCII_jason_reseq	1.171	-0.396
Isoniazid02	-0.781	0.054
Rifampicin4	-1.362	0.1
Ethambutol3	-0.741	-0.474
Meropenem3	-0.521	-0.724
Vancomycin16	-0.783	0.292
Rv2680_day32	-0.799	-0.423
H37Rv_KO_MarP	0.04	0.796
hypoxia_3wks	-3.369	-0.159
hypoxia_6wks	-2.648	-1.566
glycerol	-0.167	1.164
cholesterol	-1.3	0.835
AJ	-0.425	0.299
Bibs02	-0.539	-0.517
Bibs02c	0.144	0.0
BL6	1.166	0.575
BL6a	0.263	-0.422
BXD01	0.677	0.552
BXD010	0.399	-0.072
BXD011	0.494	0.63
BXD03	0.301	0.998
BXD04	-0.033	-0.305
BXD05	-0.086	0.269
BXD06	0.297	0.438
BXD07	0.562	0.637
BXD08	0.602	0.139
BXD09	0.429	0.81
CAST	0.12	0.707
CCcont	0.633	0.997
DS01	0.041	0.725
DS02	-1.186	0.714
DS04	0.417	0.474
DS0c	0.149	0.058
GP01	-1.522	-1.378
GP02	-0.898	-1.078
GP0c	0.27	-1.263
NOD	0.516	3.207
NZO	-0.224	0.487
PWK	-0.487	0.794
H37Rv_KO_CtpC	0.698	0.169
H37Rv_KO_CtpD	-0.71	-0.85
H37Rv_KO_Rv1272	0.476	-0.74
H37Rv_KO_SugABC	1.505	0.152
H37Rv_KO_MbtN	0.399	-1.242
Trans05	-0.325	-0.074
macrophage_unactivated	-0.436	1.411
IL1	-0.457	0.632
Rapamycin	0.74	1.145
Tcell	0.746	2.379
GMCSF	0.0	0.985
IFNab	0.692	0.81
IFNg	0.612	2.157
IFNg_GMCSF1	0.984	0.842
Rv1432_day32	0.073	0.321
Rv1565c_day32	1.264	1.03
secA2_input	-0.454	0.2
delta_Rv3594	0.26	1.216
delta_Rv3717	-0.216	0.938
delta_Rv3811	0.229	-0.269
delta_Rv0954	1.689	0.207
PonA1	-0.223	1.027
EccD1_KO	1.246	1.868
EspI_KO	0.633	1.218
PE35_KO	0.648	1.657
PPE68_KO	0.486	2.326
glycerol2	0.736	2.058
lignocerate	1.136	2.828
oleate	0.469	-0.163
phosphatidylcholine	0.958	2.417
acetate	1.589	4.234
glucAc	1.487	3.129
Rv0950ko	-0.543	-0.175
Rv1096ko	0.154	1.056
Rv3684ko	-1.431	-0.806
delta_otsA_trehalose	-1.061	0.15