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 Rv3394c/-:

update plot	correlation	link to info on gene
Rv3511/PE_PGRS55	(cc=0.5008)	info on Rv3511/PE_PGRS55
Rv3514/PE_PGRS57	(cc=0.4562)	info on Rv3514/PE_PGRS57
Rv3508/PE_PGRS54	(cc=0.4517)	info on Rv3508/PE_PGRS54
Rv2853/PE_PGRS48	(cc=0.4274)	info on Rv2853/PE_PGRS48
Rv2431c/PE25	(cc=0.405)	info on Rv2431c/PE25
Rv0834c/PE_PGRS14	(cc=0.4013)	info on Rv0834c/PE_PGRS14
Rv0142/-	(cc=0.3995)	info on Rv0142/-
Rv3299c/atsB	(cc=0.399)	info on Rv3299c/atsB
Rv0858c/dapC	(cc=0.3974)	info on Rv0858c/dapC
Rv3470c/ilvB2	(cc=0.3907)	info on Rv3470c/ilvB2

Correlation of Rv3394c/- with Rv2853/PE_PGRS48

Normalized LFCs for Rv3394c/-:
(description and provenance of datasets)

	Rv3394c/-	Rv2853/PE_PGRS48
Fe_supp_jason_reseq	-0.829	0.641
low_pH_jason_reseq	1.228	-0.269
NO_jason_reseq	0.591	0.06
B6_jason_reseq	-1.269	-0.414
MHCII_jason_reseq	-0.58	-0.425
Isoniazid02	-0.339	-0.965
Rifampicin4	0.72	0.095
Ethambutol3	-0.197	0.258
Meropenem3	0.207	-1.22
Vancomycin16	0.0	-0.788
Rv2680_day32	-0.422	-0.666
H37Rv_KO_MarP	0.289	-0.206
hypoxia_3wks	0.439	-0.335
hypoxia_6wks	-0.048	-0.72
glycerol	2.058	0.587
cholesterol	1.696	0.29
AJ	1.627	0.881
Bibs02	0.0	0.199
Bibs02c	0.756	0.273
BL6	0.16	0.488
BL6a	0.443	0.462
BXD01	0.029	0.269
BXD010	0.4	0.324
BXD011	0.137	0.519
BXD03	0.399	0.679
BXD04	0.486	0.39
BXD05	0.373	0.242
BXD06	0.417	0.507
BXD07	0.232	0.494
BXD08	1.2	0.497
BXD09	0.39	0.213
CAST	0.385	0.475
CCcont	0.677	0.574
DS01	0.777	0.24
DS02	0.364	-0.408
DS04	1.147	0.623
DS0c	-0.823	0.0
GP01	1.305	-0.129
GP02	1.89	0.108
GP0c	0.769	-0.182
NOD	-0.158	0.61
NZO	0.446	0.344
PWK	0.0	0.078
H37Rv_KO_CtpC	0.587	0.235
H37Rv_KO_CtpD	0.351	0.174
H37Rv_KO_Rv1272	1.115	0.811
H37Rv_KO_SugABC	0.659	-0.084
H37Rv_KO_MbtN	-0.024	0.659
Trans05	1.567	1.389
macrophage_unactivated	-0.114	-0.262
IL1	0.727	-0.196
Rapamycin	-0.055	-0.227
Tcell	-0.554	-0.381
GMCSF	0.317	-0.404
IFNab	-0.109	-0.435
IFNg	0.406	-0.043
IFNg_GMCSF1	1.09	-0.182
Rv1432_day32	1.112	-0.018
Rv1565c_day32	1.887	1.512
secA2_input	0.269	-0.747
delta_Rv3594	-0.078	-0.017
delta_Rv3717	0.062	0.169
delta_Rv3811	0.073	0.271
delta_Rv0954	0.124	-0.42
PonA1	0.329	0.667
EccD1_KO	0.753	0.0
EspI_KO	-0.322	0.493
PE35_KO	-0.137	0.175
PPE68_KO	0.099	-0.134
glycerol2	-0.059	-0.078
lignocerate	0.499	0.444
oleate	0.274	-0.016
phosphatidylcholine	0.296	0.245
acetate	0.733	0.053
glucAc	0.307	0.15
Rv0950ko	0.1	0.283
Rv1096ko	0.473	0.654
Rv3684ko	1.52	0.845
delta_otsA_trehalose	-0.045	0.127