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 Rv2914c/pknI

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

	Rv0134/ephF	Rv2914c/pknI
Fe_supp_jason_reseq	-0.568	-0.177
low_pH_jason_reseq	-0.688	0.187
NO_jason_reseq	0.391	-0.318
B6_jason_reseq	0.413	-0.235
MHCII_jason_reseq	0.941	0.459
Isoniazid02	-0.345	0.211
Rifampicin4	0.0	0.474
Ethambutol3	-0.461	-0.258
Meropenem3	0.271	0.21
Vancomycin16	-0.273	-0.058
Rv2680_day32	-0.09	0.131
H37Rv_KO_MarP	0.213	-0.047
hypoxia_3wks	-0.478	-0.148
hypoxia_6wks	-0.106	-0.322
glycerol	0.168	0.347
cholesterol	-0.859	-1.024
AJ	0.077	0.292
Bibs02	-0.449	0.661
Bibs02c	0.759	1.002
BL6	0.587	-0.155
BL6a	0.639	0.781
BXD01	-0.265	-0.259
BXD010	-0.255	-0.348
BXD011	0.421	-0.133
BXD03	0.226	-0.24
BXD04	-0.24	-0.153
BXD05	0.463	0.163
BXD06	0.175	-0.047
BXD07	-0.048	-0.246
BXD08	0.152	0.015
BXD09	0.292	-0.128
CAST	0.792	0.384
CCcont	-0.331	-0.573
DS01	0.229	0.224
DS02	0.249	-0.143
DS04	1.152	-0.24
DS0c	0.445	0.352
GP01	0.371	0.236
GP02	1.127	0.823
GP0c	0.279	0.0
NOD	0.404	-0.026
NZO	0.345	0.705
PWK	0.566	0.034
H37Rv_KO_CtpC	-0.114	-0.245
H37Rv_KO_CtpD	-0.348	-0.585
H37Rv_KO_Rv1272	-0.224	-0.949
H37Rv_KO_SugABC	0.588	0.11
H37Rv_KO_MbtN	0.961	1.005
Trans05	-0.302	-0.604
macrophage_unactivated	0.069	-0.597
IL1	0.018	0.0
Rapamycin	-0.034	0.025
Tcell	0.072	-0.205
GMCSF	1.098	0.388
IFNab	-0.121	0.094
IFNg	0.596	-0.126
IFNg_GMCSF1	1.037	0.977
Rv1432_day32	0.224	0.551
Rv1565c_day32	0.188	0.218
secA2_input	0.297	0.8
delta_Rv3594	-0.197	0.13
delta_Rv3717	0.127	0.599
delta_Rv3811	-0.132	0.296
delta_Rv0954	-0.098	0.032
PonA1	0.698	0.279
EccD1_KO	0.421	-0.523
EspI_KO	-0.351	0.297
PE35_KO	-0.621	0.0
PPE68_KO	-0.682	-0.47
glycerol2	0.265	-0.663
lignocerate	0.952	0.25
oleate	-0.6	-0.318
phosphatidylcholine	0.326	0.0
acetate	0.51	-0.083
glucAc	0.706	0.671
Rv0950ko	0.986	0.196
Rv1096ko	1.692	1.01
Rv3684ko	1.657	0.282
delta_otsA_trehalose	-0.613	-1.165