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 Rv2276/cyp121

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

	Rv3301c/phoY1	Rv2276/cyp121
Fe_supp_jason_reseq	0.633	0.439
low_pH_jason_reseq	-0.515	-0.052
NO_jason_reseq	0.189	-0.806
B6_jason_reseq	-0.846	-0.341
MHCII_jason_reseq	1.171	0.367
Isoniazid02	-0.781	-0.042
Rifampicin4	-1.362	-0.241
Ethambutol3	-0.741	-0.306
Meropenem3	-0.521	-0.474
Vancomycin16	-0.783	0.223
Rv2680_day32	-0.799	-0.449
H37Rv_KO_MarP	0.04	-0.26
hypoxia_3wks	-3.369	-0.403
hypoxia_6wks	-2.648	-1.247
glycerol	-0.167	0.237
cholesterol	-1.3	0.233
AJ	-0.425	1.133
Bibs02	-0.539	0.55
Bibs02c	0.144	-0.277
BL6	1.166	1.637
BL6a	0.263	0.936
BXD01	0.677	1.007
BXD010	0.399	0.564
BXD011	0.494	0.581
BXD03	0.301	1.281
BXD04	-0.033	1.013
BXD05	-0.086	0.888
BXD06	0.297	1.393
BXD07	0.562	0.491
BXD08	0.602	1.581
BXD09	0.429	1.36
CAST	0.12	0.42
CCcont	0.633	1.89
DS01	0.041	0.479
DS02	-1.186	0.158
DS04	0.417	0.472
DS0c	0.149	0.693
GP01	-1.522	0.678
GP02	-0.898	-0.384
GP0c	0.27	0.094
NOD	0.516	1.988
NZO	-0.224	0.097
PWK	-0.487	0.142
H37Rv_KO_CtpC	0.698	1.918
H37Rv_KO_CtpD	-0.71	0.516
H37Rv_KO_Rv1272	0.476	0.931
H37Rv_KO_SugABC	1.505	1.332
H37Rv_KO_MbtN	0.399	-0.108
Trans05	-0.325	1.265
macrophage_unactivated	-0.436	0.859
IL1	-0.457	-0.617
Rapamycin	0.74	-0.338
Tcell	0.746	0.541
GMCSF	0.0	-0.444
IFNab	0.692	-0.109
IFNg	0.612	0.045
IFNg_GMCSF1	0.984	-0.226
Rv1432_day32	0.073	-0.143
Rv1565c_day32	1.264	-0.599
secA2_input	-0.454	-1.486
delta_Rv3594	0.26	-0.623
delta_Rv3717	-0.216	-1.106
delta_Rv3811	0.229	0.44
delta_Rv0954	1.689	-0.441
PonA1	-0.223	0.684
EccD1_KO	1.246	0.21
EspI_KO	0.633	2.193
PE35_KO	0.648	2.129
PPE68_KO	0.486	1.872
glycerol2	0.736	1.864
lignocerate	1.136	2.12
oleate	0.469	0.169
phosphatidylcholine	0.958	1.84
acetate	1.589	2.369
glucAc	1.487	1.957
Rv0950ko	-0.543	0.06
Rv1096ko	0.154	0.06
Rv3684ko	-1.431	-0.416
delta_otsA_trehalose	-1.061	1.275