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 Rv2737c/recA:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv0003/recF	(cc=0.8067)	info on Rv0003/recF
Rv1638/uvrA	(cc=0.7245)	info on Rv1638/uvrA
Rv3261/fbiA	(cc=0.6803)	info on Rv3261/fbiA
Rv1432/-	(cc=0.6644)	info on Rv1432/-
Rv2362c/recO	(cc=0.6571)	info on Rv2362c/recO
Rv1633/uvrB	(cc=0.6527)	info on Rv1633/uvrB
Rv2535c/pepQ	(cc=0.6427)	info on Rv2535c/pepQ
Rv3193c/-	(cc=0.6309)	info on Rv3193c/-
Rv2894c/xerC	(cc=0.6309)	info on Rv2894c/xerC
Rv1701/-	(cc=0.6242)	info on Rv1701/-

Correlation of Rv2737c/recA with Rv0003/recF

Normalized LFCs for Rv2737c/recA:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv2737c/recA	Rv0003/recF
Fe_supp_jason_reseq	3.01	2.382
low_pH_jason_reseq	0.768	0.0
NO_jason_reseq	0.446	0.281
B6_jason_reseq	0.0	0.333
MHCII_jason_reseq	0.166	0.0
Isoniazid02	0.358	0.063
Rifampicin4	-0.563	-1.086
Ethambutol3	0.314	-0.288
Meropenem3	-0.188	-0.624
Vancomycin16	-1.141	-0.913
Rv2680_day32	-0.588	-0.554
H37Rv_KO_MarP	-1.135	-0.807
hypoxia_3wks	-1.579	-1.344
hypoxia_6wks	-1.748	-1.416
glycerol	2.478	1.24
cholesterol	1.44	1.099
AJ	-0.471	-0.168
Bibs02	-0.24	-0.273
Bibs02c	-0.424	0.0
BL6	0.145	0.084
BL6a	0.438	0.696
BXD01	0.077	0.322
BXD010	0.345	0.0
BXD011	0.711	0.383
BXD03	-0.177	0.475
BXD04	0.391	0.305
BXD05	0.297	0.176
BXD06	-0.084	0.469
BXD07	0.437	0.796
BXD08	0.225	0.174
BXD09	0.566	0.494
CAST	-0.145	-0.344
CCcont	2.295	1.531
DS01	-0.149	0.159
DS02	0.252	0.147
DS04	0.0	0.37
DS0c	-0.284	0.652
GP01	-0.449	0.68
GP02	0.184	-0.06
GP0c	0.22	1.112
NOD	0.905	-0.163
NZO	0.338	0.134
PWK	-0.398	-0.142
H37Rv_KO_CtpC	-0.213	0.401
H37Rv_KO_CtpD	0.878	0.778
H37Rv_KO_Rv1272	0.568	0.185
H37Rv_KO_SugABC	1.288	1.183
H37Rv_KO_MbtN	0.576	0.069
Trans05	0.906	0.249
macrophage_unactivated	0.0	0.701
IL1	-0.831	-0.78
Rapamycin	-0.555	-0.807
Tcell	0.0	-0.267
GMCSF	0.0	0.0
IFNab	0.922	0.877
IFNg	-0.233	0.208
IFNg_GMCSF1	0.503	0.478
Rv1432_day32	-0.301	-1.005
Rv1565c_day32	-1.14	-0.362
secA2_input	-0.247	-0.714
delta_Rv3594	1.06	0.33
delta_Rv3717	-0.331	-0.542
delta_Rv3811	0.036	0.492
delta_Rv0954	0.99	0.116
PonA1	-0.175	-0.426
EccD1_KO	0.072	1.01
EspI_KO	0.188	-0.108
PE35_KO	1.75	1.155
PPE68_KO	1.363	1.078
glycerol2	-1.883	-2.152
lignocerate	-1.506	-2.157
oleate	-1.905	-2.178
phosphatidylcholine	-1.661	-2.053
acetate	0.274	-0.775
glucAc	-0.118	-0.554
Rv0950ko	-0.25	0.0
Rv1096ko	-0.338	0.899
Rv3684ko	0.174	0.377
delta_otsA_trehalose	1.013	-0.711