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 Rv3429/PPE59:

update plot	correlation	link to info on gene
Rv2929/-	(cc=0.7601)	info on Rv2929/-
Rv1500/-	(cc=0.7176)	info on Rv1500/-
Rv3378c/-	(cc=0.6567)	info on Rv3378c/-
Rv2430c/PPE41	(cc=0.6426)	info on Rv2430c/PPE41
Rv3383c/idsB	(cc=0.6388)	info on Rv3383c/idsB
Rv1059/-	(cc=0.6347)	info on Rv1059/-
Rv3142c/-	(cc=0.6084)	info on Rv3142c/-
Rv0403c/mmpS1	(cc=0.6068)	info on Rv0403c/mmpS1
Rv1507c/-	(cc=0.5931)	info on Rv1507c/-
Rv0059/-	(cc=0.5908)	info on Rv0059/-

Correlation of Rv3429/PPE59 with Rv2929/-

Normalized LFCs for Rv3429/PPE59:
(description and provenance of datasets)

	Rv3429/PPE59	Rv2929/-
Fe_supp_jason_reseq	0.628	-0.775
low_pH_jason_reseq	0.202	0.059
NO_jason_reseq	-0.029	1.113
B6_jason_reseq	-1.06	-2.004
MHCII_jason_reseq	0.265	-2.323
Isoniazid02	-0.125	1.192
Rifampicin4	-0.566	0.054
Ethambutol3	1.225	1.395
Meropenem3	1.438	0.954
Vancomycin16	0.215	0.355
Rv2680_day32	-0.23	-2.504
H37Rv_KO_MarP	0.346	-0.373
hypoxia_3wks	0.0	0.072
hypoxia_6wks	0.069	0.013
glycerol	-1.568	-1.194
cholesterol	-0.909	0.171
AJ	0.382	0.598
Bibs02	-0.276	-1.952
Bibs02c	0.412	0.485
BL6	1.223	0.745
BL6a	1.017	1.333
BXD01	1.398	1.192
BXD010	1.497	1.561
BXD011	1.714	1.183
BXD03	0.988	1.942
BXD04	0.307	0.985
BXD05	1.232	1.564
BXD06	1.426	1.66
BXD07	1.178	1.048
BXD08	1.307	0.596
BXD09	1.463	1.566
CAST	0.379	0.754
CCcont	0.942	0.525
DS01	0.77	0.417
DS02	0.668	0.225
DS04	1.026	0.587
DS0c	0.728	0.839
GP01	1.468	1.223
GP02	0.874	0.686
GP0c	1.149	0.503
NOD	0.443	1.08
NZO	0.516	0.783
PWK	0.602	0.261
H37Rv_KO_CtpC	1.547	1.8
H37Rv_KO_CtpD	1.898	2.176
H37Rv_KO_Rv1272	0.86	1.204
H37Rv_KO_SugABC	1.451	1.845
H37Rv_KO_MbtN	0.74	-0.188
Trans05	1.42	1.382
macrophage_unactivated	0.417	0.54
IL1	0.658	0.638
Rapamycin	-0.203	-0.405
Tcell	1.121	0.394
GMCSF	-0.412	-0.731
IFNab	-0.411	-0.417
IFNg	0.216	0.12
IFNg_GMCSF1	-0.459	0.0
Rv1432_day32	0.09	0.314
Rv1565c_day32	-1.088	-1.14
secA2_input	-0.399	-0.589
delta_Rv3594	-0.722	-1.502
delta_Rv3717	-0.812	-0.599
delta_Rv3811	-0.366	-0.565
delta_Rv0954	-0.397	-0.432
PonA1	-0.518	-0.829
EccD1_KO	0.224	-0.053
EspI_KO	0.408	0.704
PE35_KO	0.548	0.277
PPE68_KO	0.189	0.0
glycerol2	0.426	0.06
lignocerate	0.591	0.2
oleate	0.417	0.149
phosphatidylcholine	0.916	0.37
acetate	0.472	1.199
glucAc	0.483	-0.133
Rv0950ko	0.422	0.594
Rv1096ko	-0.582	-1.224
Rv3684ko	-0.54	-0.619
delta_otsA_trehalose	0.083	-0.459