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 Rv0648/-

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

	Rv0134/ephF	Rv0648/-
Fe_supp_jason_reseq	-0.568	-0.423
low_pH_jason_reseq	-0.688	-0.159
NO_jason_reseq	0.391	-0.06
B6_jason_reseq	0.413	0.75
MHCII_jason_reseq	0.941	0.848
Isoniazid02	-0.345	0.311
Rifampicin4	0.0	0.485
Ethambutol3	-0.461	0.174
Meropenem3	0.271	0.625
Vancomycin16	-0.273	-0.077
Rv2680_day32	-0.09	0.089
H37Rv_KO_MarP	0.213	0.251
hypoxia_3wks	-0.478	0.124
hypoxia_6wks	-0.106	0.127
glycerol	0.168	1.027
cholesterol	-0.859	0.486
AJ	0.077	0.624
Bibs02	-0.449	0.148
Bibs02c	0.759	0.374
BL6	0.587	0.278
BL6a	0.639	-0.053
BXD01	-0.265	-0.387
BXD010	-0.255	-0.353
BXD011	0.421	-0.149
BXD03	0.226	-0.036
BXD04	-0.24	-0.124
BXD05	0.463	0.102
BXD06	0.175	-0.164
BXD07	-0.048	-0.154
BXD08	0.152	0.055
BXD09	0.292	-0.341
CAST	0.792	0.454
CCcont	-0.331	-0.201
DS01	0.229	0.756
DS02	0.249	0.548
DS04	1.152	1.15
DS0c	0.445	0.492
GP01	0.371	0.365
GP02	1.127	0.819
GP0c	0.279	0.238
NOD	0.404	0.5
NZO	0.345	0.426
PWK	0.566	0.253
H37Rv_KO_CtpC	-0.114	-0.331
H37Rv_KO_CtpD	-0.348	0.762
H37Rv_KO_Rv1272	-0.224	-0.371
H37Rv_KO_SugABC	0.588	0.753
H37Rv_KO_MbtN	0.961	-0.022
Trans05	-0.302	0.034
macrophage_unactivated	0.069	-0.603
IL1	0.018	0.314
Rapamycin	-0.034	-0.193
Tcell	0.072	-0.622
GMCSF	1.098	0.211
IFNab	-0.121	0.042
IFNg	0.596	-0.305
IFNg_GMCSF1	1.037	0.022
Rv1432_day32	0.224	-0.242
Rv1565c_day32	0.188	0.27
secA2_input	0.297	0.969
delta_Rv3594	-0.197	0.754
delta_Rv3717	0.127	0.673
delta_Rv3811	-0.132	0.344
delta_Rv0954	-0.098	0.098
PonA1	0.698	0.188
EccD1_KO	0.421	0.437
EspI_KO	-0.351	-0.094
PE35_KO	-0.621	-0.324
PPE68_KO	-0.682	-0.47
glycerol2	0.265	0.154
lignocerate	0.952	0.639
oleate	-0.6	0.237
phosphatidylcholine	0.326	0.282
acetate	0.51	0.387
glucAc	0.706	0.468
Rv0950ko	0.986	0.386
Rv1096ko	1.692	1.276
Rv3684ko	1.657	0.108
delta_otsA_trehalose	-0.613	-0.912