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 Rv3297/nei:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv2340c/PE_PGRS39	(cc=0.5435)	info on Rv2340c/PE_PGRS39
Rv2326c/-	(cc=0.5186)	info on Rv2326c/-
Rv1243c/PE_PGRS23	(cc=0.4979)	info on Rv1243c/PE_PGRS23
Rv1066/-	(cc=0.4936)	info on Rv1066/-
Rv2490c/PE_PGRS43	(cc=0.4751)	info on Rv2490c/PE_PGRS43
Rv0648/-	(cc=0.4718)	info on Rv0648/-
Rv2974c/-	(cc=0.4703)	info on Rv2974c/-
Rv0614/-	(cc=0.4674)	info on Rv0614/-
Rv2402/-	(cc=0.4649)	info on Rv2402/-
Rv2646/-	(cc=0.4589)	info on Rv2646/-

Correlation of Rv3297/nei with Rv2340c/PE_PGRS39

Normalized LFCs for Rv3297/nei:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3297/nei	Rv2340c/PE_PGRS39
Fe_supp_jason_reseq	-0.224	-0.063
low_pH_jason_reseq	-0.04	-0.452
NO_jason_reseq	-0.305	-0.417
B6_jason_reseq	-0.009	0.657
MHCII_jason_reseq	0.031	0.619
Isoniazid02	0.16	1.157
Rifampicin4	1.248	0.485
Ethambutol3	1.927	1.549
Meropenem3	0.707	0.728
Vancomycin16	0.661	0.061
Rv2680_day32	0.764	-0.465
H37Rv_KO_MarP	0.178	-0.302
hypoxia_3wks	-0.566	-0.774
hypoxia_6wks	-0.319	-0.666
glycerol	0.487	0.65
cholesterol	0.424	0.315
AJ	-0.072	0.565
Bibs02	0.787	0.984
Bibs02c	-0.361	0.679
BL6	0.25	-0.16
BL6a	-0.452	0.014
BXD01	-0.148	-0.58
BXD010	-0.403	-0.687
BXD011	-0.464	-0.737
BXD03	0.007	-0.566
BXD04	-1.029	0.035
BXD05	0.303	-0.068
BXD06	-0.486	-0.939
BXD07	-0.425	-0.624
BXD08	-0.67	-0.277
BXD09	-0.553	-0.626
CAST	0.103	0.794
CCcont	-0.031	-0.278
DS01	0.867	0.956
DS02	1.065	0.993
DS04	1.106	0.45
DS0c	1.398	0.94
GP01	-0.01	-0.24
GP02	1.55	0.643
GP0c	-0.531	-0.111
NOD	0.542	-0.218
NZO	-0.094	0.48
PWK	-0.01	0.672
H37Rv_KO_CtpC	-0.726	-0.891
H37Rv_KO_CtpD	-0.006	-0.009
H37Rv_KO_Rv1272	-1.157	0.232
H37Rv_KO_SugABC	-0.015	0.386
H37Rv_KO_MbtN	0.249	0.239
Trans05	0.423	0.28
macrophage_unactivated	-0.758	-1.004
IL1	-0.187	-0.736
Rapamycin	-0.279	-0.62
Tcell	-0.714	-0.978
GMCSF	0.092	-0.747
IFNab	-0.333	-0.429
IFNg	-0.168	-0.526
IFNg_GMCSF1	1.128	-0.154
Rv1432_day32	0.057	0.352
Rv1565c_day32	-1.829	0.051
secA2_input	0.676	0.512
delta_Rv3594	0.061	-0.207
delta_Rv3717	-0.273	-0.44
delta_Rv3811	-0.174	-0.007
delta_Rv0954	-0.063	0.172
PonA1	-0.328	-0.128
EccD1_KO	-0.322	0.697
EspI_KO	-0.453	0.211
PE35_KO	0.108	0.117
PPE68_KO	0.749	0.038
glycerol2	-0.338	-0.041
lignocerate	0.412	0.516
oleate	-0.315	0.0
phosphatidylcholine	0.15	0.494
acetate	0.874	0.116
glucAc	0.642	0.086
Rv0950ko	-0.371	0.555
Rv1096ko	0.175	-0.537
Rv3684ko	-0.131	-0.442
delta_otsA_trehalose	-1.502	-0.722