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 Rv0134/ephF:

update plot	correlation	link to info on gene
Rv2914c/pknI	(cc=0.549)	info on Rv2914c/pknI
Rv3896c/-	(cc=0.5341)	info on Rv3896c/-
Rv0327c/cyp135A1	(cc=0.5183)	info on Rv0327c/cyp135A1
Rv3026c/-	(cc=0.504)	info on Rv3026c/-
Rv0530/-	(cc=0.4818)	info on Rv0530/-
Rv3786c/-	(cc=0.4778)	info on Rv3786c/-
Rv3522/ltp4	(cc=0.473)	info on Rv3522/ltp4
Rv0897c/-	(cc=0.4604)	info on Rv0897c/-
Rv0858c/dapC	(cc=0.4531)	info on Rv0858c/dapC
Rv0648/-	(cc=0.4515)	info on Rv0648/-

Correlation of Rv0134/ephF with Rv0858c/dapC

Normalized LFCs for Rv0134/ephF:
(description and provenance of datasets)

	Rv0134/ephF	Rv0858c/dapC
Fe_supp_jason_reseq	-0.568	-0.704
low_pH_jason_reseq	-0.688	-0.611
NO_jason_reseq	0.391	-0.249
B6_jason_reseq	0.413	-0.034
MHCII_jason_reseq	0.941	0.309
Isoniazid02	-0.345	0.418
Rifampicin4	0.0	0.471
Ethambutol3	-0.461	-0.049
Meropenem3	0.271	0.344
Vancomycin16	-0.273	0.761
Rv2680_day32	-0.09	-0.636
H37Rv_KO_MarP	0.213	0.172
hypoxia_3wks	-0.478	0.638
hypoxia_6wks	-0.106	0.171
glycerol	0.168	0.202
cholesterol	-0.859	0.014
AJ	0.077	0.25
Bibs02	-0.449	0.0
Bibs02c	0.759	0.039
BL6	0.587	0.157
BL6a	0.639	0.198
BXD01	-0.265	0.012
BXD010	-0.255	0.182
BXD011	0.421	-0.359
BXD03	0.226	-0.12
BXD04	-0.24	0.176
BXD05	0.463	0.145
BXD06	0.175	0.386
BXD07	-0.048	0.161
BXD08	0.152	-0.133
BXD09	0.292	0.513
CAST	0.792	-0.404
CCcont	-0.331	0.237
DS01	0.229	0.698
DS02	0.249	0.38
DS04	1.152	1.02
DS0c	0.445	-0.063
GP01	0.371	0.491
GP02	1.127	0.675
GP0c	0.279	0.966
NOD	0.404	-0.021
NZO	0.345	0.795
PWK	0.566	-0.301
H37Rv_KO_CtpC	-0.114	0.647
H37Rv_KO_CtpD	-0.348	-0.618
H37Rv_KO_Rv1272	-0.224	0.366
H37Rv_KO_SugABC	0.588	0.593
H37Rv_KO_MbtN	0.961	-0.828
Trans05	-0.302	0.909
macrophage_unactivated	0.069	0.114
IL1	0.018	0.415
Rapamycin	-0.034	-0.037
Tcell	0.072	-0.039
GMCSF	1.098	-0.066
IFNab	-0.121	0.62
IFNg	0.596	0.489
IFNg_GMCSF1	1.037	1.027
Rv1432_day32	0.224	0.231
Rv1565c_day32	0.188	0.698
secA2_input	0.297	0.637
delta_Rv3594	-0.197	-0.217
delta_Rv3717	0.127	-0.097
delta_Rv3811	-0.132	-0.617
delta_Rv0954	-0.098	0.167
PonA1	0.698	0.492
EccD1_KO	0.421	0.569
EspI_KO	-0.351	-0.442
PE35_KO	-0.621	-0.531
PPE68_KO	-0.682	0.077
glycerol2	0.265	0.524
lignocerate	0.952	0.951
oleate	-0.6	-0.485
phosphatidylcholine	0.326	0.847
acetate	0.51	0.542
glucAc	0.706	0.925
Rv0950ko	0.986	0.482
Rv1096ko	1.692	1.677
Rv3684ko	1.657	1.385
delta_otsA_trehalose	-0.613	0.286