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 Rv3478/PPE60:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv3479/-	(cc=0.5427)	info on Rv3479/-
Rv1523/-	(cc=0.5356)	info on Rv1523/-
Rv2517c/-	(cc=0.507)	info on Rv2517c/-
Rv0888/-	(cc=0.491)	info on Rv0888/-
Rv2556c/-	(cc=0.4787)	info on Rv2556c/-
Rv2332/mez	(cc=0.4784)	info on Rv2332/mez
Rv1803c/PE_PGRS32	(cc=0.4726)	info on Rv1803c/PE_PGRS32
Rv3059/cyp136	(cc=0.4557)	info on Rv3059/cyp136
Rv2659c/-	(cc=0.4538)	info on Rv2659c/-
Rv0089/-	(cc=0.4531)	info on Rv0089/-

Correlation of Rv3478/PPE60 with Rv3479/-

Normalized LFCs for Rv3478/PPE60:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3478/PPE60	Rv3479/-
Fe_supp_jason_reseq	-0.627	-0.426
low_pH_jason_reseq	-0.31	-0.544
NO_jason_reseq	-0.509	0.173
B6_jason_reseq	-0.499	0.097
MHCII_jason_reseq	-0.12	0.155
Isoniazid02	0.259	0.955
Rifampicin4	0.301	-0.428
Ethambutol3	0.637	1.175
Meropenem3	-0.805	1.544
Vancomycin16	-0.738	-0.419
Rv2680_day32	1.156	1.463
H37Rv_KO_MarP	0.94	0.374
hypoxia_3wks	-0.658	-1.372
hypoxia_6wks	-0.921	-0.591
glycerol	-1.76	0.212
cholesterol	-1.858	-0.55
AJ	0.096	0.398
Bibs02	-0.326	-0.658
Bibs02c	-0.577	-0.596
BL6	-0.581	0.051
BL6a	-0.561	-0.294
BXD01	-0.462	-0.009
BXD010	-0.15	-0.15
BXD011	-0.452	-0.082
BXD03	-1.083	-0.168
BXD04	-0.275	0.357
BXD05	-0.065	0.175
BXD06	-0.698	-0.126
BXD07	-0.392	-0.119
BXD08	-0.414	-0.241
BXD09	-1.048	0.0
CAST	0.048	0.475
CCcont	0.008	-0.118
DS01	-0.802	-0.37
DS02	-0.011	-0.046
DS04	-0.346	-0.197
DS0c	-0.57	-0.091
GP01	0.232	-0.071
GP02	-1.328	0.045
GP0c	-1.284	-0.765
NOD	0.911	0.016
NZO	0.182	0.478
PWK	0.206	0.371
H37Rv_KO_CtpC	-0.472	-0.294
H37Rv_KO_CtpD	-1.876	0.109
H37Rv_KO_Rv1272	-0.269	-0.73
H37Rv_KO_SugABC	-0.099	0.17
H37Rv_KO_MbtN	-0.243	0.594
Trans05	0.823	-0.055
macrophage_unactivated	-1.054	-0.278
IL1	-0.243	0.062
Rapamycin	-0.252	-0.132
Tcell	-0.13	-0.593
GMCSF	-1.302	0.219
IFNab	-0.441	-0.372
IFNg	-0.604	0.056
IFNg_GMCSF1	-0.459	-0.277
Rv1432_day32	2.139	2.477
Rv1565c_day32	0.055	0.603
secA2_input	0.05	0.33
delta_Rv3594	0.162	-0.106
delta_Rv3717	0.258	-0.064
delta_Rv3811	-0.399	0.073
delta_Rv0954	0.567	0.318
PonA1	0.92	0.701
EccD1_KO	0.799	0.918
EspI_KO	0.77	0.91
PE35_KO	1.047	1.114
PPE68_KO	0.893	0.675
glycerol2	-0.517	0.202
lignocerate	0.141	0.25
oleate	-0.164	-0.457
phosphatidylcholine	1.605	-0.14
acetate	-0.574	-0.19
glucAc	-0.595	0.096
Rv0950ko	-0.467	-0.621
Rv1096ko	-0.253	0.434
Rv3684ko	-0.478	-0.524
delta_otsA_trehalose	-1.319	-0.083