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 Rv3865/espF:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv0456c/echA2	(cc=0.4111)	info on Rv0456c/echA2
Rv2154c/ftsW	(cc=0.4023)	info on Rv2154c/ftsW
Rv2305/-	(cc=0.376)	info on Rv2305/-
Rv0785/-	(cc=0.3732)	info on Rv0785/-
Rv2083/-	(cc=0.3657)	info on Rv2083/-
Rv2860c/glnA4	(cc=0.3577)	info on Rv2860c/glnA4
Rv3039c/echA17	(cc=0.3572)	info on Rv3039c/echA17
Rv2806/-	(cc=0.356)	info on Rv2806/-
Rv2579/dhaA	(cc=0.3481)	info on Rv2579/dhaA
Rv2832c/ugpC	(cc=0.3441)	info on Rv2832c/ugpC

Correlation of Rv3865/espF with Rv0456c/echA2

Normalized LFCs for Rv3865/espF:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3865/espF	Rv0456c/echA2
Fe_supp_jason_reseq	-0.646	-0.047
low_pH_jason_reseq	-1.33	-0.427
NO_jason_reseq	-2.494	-0.764
B6_jason_reseq	0.456	0.514
MHCII_jason_reseq	0.215	0.323
Isoniazid02	-0.909	-0.349
Rifampicin4	0.168	-0.057
Ethambutol3	1.557	-0.103
Meropenem3	0.019	-0.268
Vancomycin16	-0.639	0.215
Rv2680_day32	-0.142	0.328
H37Rv_KO_MarP	0.443	-0.212
hypoxia_3wks	0.247	-0.096
hypoxia_6wks	-0.867	-0.566
glycerol	-0.8	0.92
cholesterol	-1.263	0.064
AJ	1.168	0.556
Bibs02	-1.653	-0.388
Bibs02c	0.665	0.615
BL6	0.115	-0.422
BL6a	0.231	0.099
BXD01	-0.416	0.244
BXD010	0.611	-0.614
BXD011	-0.455	-0.111
BXD03	-0.037	0.018
BXD04	-0.243	-0.532
BXD05	-0.589	-0.318
BXD06	0.503	0.199
BXD07	0.196	0.4
BXD08	-0.283	-0.414
BXD09	0.112	-0.344
CAST	-1.261	0.839
CCcont	0.061	-0.089
DS01	1.56	-0.358
DS02	1.112	0.276
DS04	-0.11	0.364
DS0c	1.812	0.041
GP01	-0.83	-1.084
GP02	0.306	1.232
GP0c	-0.682	-1.168
NOD	-0.226	0.015
NZO	1.228	1.165
PWK	3.434	1.653
H37Rv_KO_CtpC	-0.644	1.001
H37Rv_KO_CtpD	-1.703	-0.545
H37Rv_KO_Rv1272	-0.588	-0.452
H37Rv_KO_SugABC	-0.565	-0.334
H37Rv_KO_MbtN	-0.368	-0.164
Trans05	-0.492	-0.55
macrophage_unactivated	1.253	0.732
IL1	-1.178	-0.62
Rapamycin	0.218	-0.328
Tcell	0.176	0.218
GMCSF	0.861	-0.38
IFNab	-0.054	-0.033
IFNg	-0.15	-0.353
IFNg_GMCSF1	0.057	-0.87
Rv1432_day32	0.0	0.535
Rv1565c_day32	0.463	1.256
secA2_input	1.338	0.091
delta_Rv3594	1.424	0.878
delta_Rv3717	1.1	-0.175
delta_Rv3811	1.109	0.177
delta_Rv0954	-0.34	-0.088
PonA1	-1.543	-0.511
EccD1_KO	-0.312	0.599
EspI_KO	-0.151	0.459
PE35_KO	0.368	0.49
PPE68_KO	-0.259	0.515
glycerol2	-0.528	0.474
lignocerate	-1.274	0.106
oleate	-0.286	0.152
phosphatidylcholine	-0.627	0.331
acetate	-1.026	0.199
glucAc	-1.221	-0.42
Rv0950ko	-0.582	-1.423
Rv1096ko	-0.582	-1.472
Rv3684ko	-0.586	-1.235
delta_otsA_trehalose	-0.887	0.774