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 Rv3876/espI:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv3882c/eccE1	(cc=0.7228)	info on Rv3882c/eccE1
Rv3615c/espC	(cc=0.714)	info on Rv3615c/espC
Rv3871/eccCb1	(cc=0.7125)	info on Rv3871/eccCb1
Rv3869/eccB1	(cc=0.7082)	info on Rv3869/eccB1
Rv3874/esxB	(cc=0.7055)	info on Rv3874/esxB
Rv3883c/mycP1	(cc=0.6932)	info on Rv3883c/mycP1
Rv3870/eccCa1	(cc=0.6846)	info on Rv3870/eccCa1
Rv3880c/espL	(cc=0.6628)	info on Rv3880c/espL
Rv3616c/espA	(cc=0.6523)	info on Rv3616c/espA
Rv3614c/espD	(cc=0.6452)	info on Rv3614c/espD

Correlation of Rv3876/espI with Rv3882c/eccE1

Normalized LFCs for Rv3876/espI:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3876/espI	Rv3882c/eccE1
Fe_supp_jason_reseq	-0.257	-0.158
low_pH_jason_reseq	0.0	-0.681
NO_jason_reseq	-0.05	-0.137
B6_jason_reseq	-1.514	-2.577
MHCII_jason_reseq	-1.834	-2.917
Isoniazid02	0.343	-0.441
Rifampicin4	0.263	-0.758
Ethambutol3	0.957	0.265
Meropenem3	0.271	0.539
Vancomycin16	0.799	0.098
Rv2680_day32	-0.419	-3.186
H37Rv_KO_MarP	0.975	1.198
hypoxia_3wks	-0.056	-0.439
hypoxia_6wks	0.0	-0.052
glycerol	-0.484	0.015
cholesterol	-0.32	-0.207
AJ	-3.185	-5.849
Bibs02	-3.413	-6.0
Bibs02c	-2.692	-5.218
BL6	-1.51	-2.18
BL6a	-2.528	-4.305
BXD01	-1.863	-3.18
BXD010	-2.414	-2.232
BXD011	-2.288	-2.846
BXD03	-1.888	-2.565
BXD04	-0.852	-1.792
BXD05	-1.76	-3.285
BXD06	-2.591	-3.16
BXD07	-2.048	-3.123
BXD08	-2.805	-3.282
BXD09	-2.573	-3.543
CAST	-3.162	-4.96
CCcont	-0.117	-0.15
DS01	-3.585	-3.826
DS02	-2.891	-4.684
DS04	-2.114	-3.187
DS0c	-4.049	-4.084
GP01	-1.709	-2.963
GP02	-2.251	-2.747
GP0c	-0.659	-0.702
NOD	-1.24	-2.146
NZO	-2.651	-4.82
PWK	-3.028	-5.363
H37Rv_KO_CtpC	-1.289	-1.31
H37Rv_KO_CtpD	-0.575	-1.751
H37Rv_KO_Rv1272	-1.859	-3.306
H37Rv_KO_SugABC	-0.99	-0.318
H37Rv_KO_MbtN	0.726	0.692
Trans05	-1.169	-2.028
macrophage_unactivated	-1.089	-0.893
IL1	-2.411	-0.344
Rapamycin	-2.516	-0.301
Tcell	0.573	-2.017
GMCSF	-1.695	0.325
IFNab	-1.23	1.735
IFNg	-3.052	-1.748
IFNg_GMCSF1	-3.067	-1.386
Rv1432_day32	-1.31	-2.744
Rv1565c_day32	-2.751	-3.434
secA2_input	-0.088	-0.357
delta_Rv3594	-0.034	-0.121
delta_Rv3717	-0.399	-0.067
delta_Rv3811	-0.159	-0.074
delta_Rv0954	-0.583	-0.023
PonA1	-1.025	-0.279
EccD1_KO	-0.178	-0.217
EspI_KO	-6.0	-0.89
PE35_KO	0.137	-0.633
PPE68_KO	-0.093	-0.448
glycerol2	0.279	0.754
lignocerate	0.537	0.869
oleate	0.166	0.679
phosphatidylcholine	0.319	0.343
acetate	-0.13	-0.126
glucAc	0.176	0.187
Rv0950ko	0.253	0.416
Rv1096ko	-0.392	-0.431
Rv3684ko	0.174	-0.576
delta_otsA_trehalose	0.046	-1.389