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 Rv2353c/PPE39:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv2275/-	(cc=0.541)	info on Rv2275/-
Rv1490/-	(cc=0.5279)	info on Rv1490/-
Rv2253/-	(cc=0.523)	info on Rv2253/-
Rv1548c/PPE21	(cc=0.5002)	info on Rv1548c/PPE21
Rv3142c/-	(cc=0.479)	info on Rv3142c/-
Rv2544/lppB	(cc=0.4687)	info on Rv2544/lppB
Rv3382c/lytB1	(cc=0.4599)	info on Rv3382c/lytB1
Rv1552/frdA	(cc=0.4598)	info on Rv1552/frdA
Rv1582c/-	(cc=0.456)	info on Rv1582c/-
Rv3112/moaD1	(cc=0.4555)	info on Rv3112/moaD1

Correlation of Rv2353c/PPE39 with Rv2275/-

Normalized LFCs for Rv2353c/PPE39:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv2353c/PPE39	Rv2275/-
Fe_supp_jason_reseq	-0.469	0.827
low_pH_jason_reseq	-0.115	0.617
NO_jason_reseq	-0.273	-0.244
B6_jason_reseq	-0.933	-0.7
MHCII_jason_reseq	-0.605	0.61
Isoniazid02	0.554	0.153
Rifampicin4	-0.382	0.975
Ethambutol3	-0.171	0.188
Meropenem3	-0.406	0.352
Vancomycin16	0.727	0.539
Rv2680_day32	-1.287	-0.471
H37Rv_KO_MarP	-0.272	0.08
hypoxia_3wks	-0.183	0.128
hypoxia_6wks	0.269	-0.288
glycerol	-0.347	-0.453
cholesterol	-0.145	0.184
AJ	0.467	0.294
Bibs02	1.044	1.13
Bibs02c	-0.988	-0.47
BL6	1.311	0.864
BL6a	0.346	0.528
BXD01	-0.085	1.203
BXD010	0.444	0.816
BXD011	0.383	1.745
BXD03	0.67	1.025
BXD04	0.039	0.0
BXD05	-0.135	0.615
BXD06	0.122	0.39
BXD07	0.601	0.602
BXD08	0.197	0.871
BXD09	-0.241	1.087
CAST	-0.669	-1.054
CCcont	0.484	1.179
DS01	-0.318	0.503
DS02	-1.137	0.142
DS04	-0.062	0.929
DS0c	-0.292	-0.231
GP01	-1.044	-0.354
GP02	0.099	-0.523
GP0c	-0.75	-0.986
NOD	1.113	-0.239
NZO	0.0	1.306
PWK	0.342	-1.232
H37Rv_KO_CtpC	0.1	1.545
H37Rv_KO_CtpD	1.481	1.255
H37Rv_KO_Rv1272	1.36	2.719
H37Rv_KO_SugABC	0.547	2.705
H37Rv_KO_MbtN	1.541	1.924
Trans05	0.263	1.729
macrophage_unactivated	0.461	1.215
IL1	-0.798	-0.089
Rapamycin	0.092	1.114
Tcell	-0.417	0.873
GMCSF	-0.338	0.51
IFNab	-1.164	0.088
IFNg	0.39	0.516
IFNg_GMCSF1	-0.965	-1.656
Rv1432_day32	-0.361	-0.411
Rv1565c_day32	0.169	0.3
secA2_input	-1.096	-1.681
delta_Rv3594	-0.503	-0.725
delta_Rv3717	-0.155	-0.927
delta_Rv3811	0.0	-0.796
delta_Rv0954	-0.978	-1.708
PonA1	-0.297	-0.936
EccD1_KO	-0.687	2.111
EspI_KO	0.231	1.443
PE35_KO	-0.251	1.17
PPE68_KO	0.259	1.872
glycerol2	0.069	0.0
lignocerate	0.38	0.505
oleate	0.201	0.0
phosphatidylcholine	0.321	0.415
acetate	0.451	1.014
glucAc	0.403	0.487
Rv0950ko	0.323	-1.354
Rv1096ko	-1.034	-0.835
Rv3684ko	-1.123	-1.179
delta_otsA_trehalose	0.069	-0.836