Supplementary Material for the manuscript:

Computational prediction of novel components of lung transcriptional networks

M. Juanita Martinez¹, Andrew D. Smith², Bilan Li¹, Michael Q. Zhang², and Kevin S. Harrod¹

¹Lovelace Respiratory Research Institute, 2425 Ridgecrest Dr. SE, Albuquerque NM 87108 USA and ²Cold Spring Harbor Laboratory, One Bungtown Rd, Cold Spring Harbor, NY 11724

Supplementary Methods - download file

Supplementary Results – download file

Supplementary files

1) Input sequences download all files

foxa2down.Hs.1200.fg

foxa2down.Mm.1200.fg

wntdown.Hs.1200.fg

wntdown.Mm.1200.fg

Random.Hs.1200.bg

Random.Mm.1200.bg

Transcripts_used.xls

2) Novel motifs download all files

foxa2down.Hs.1200.known.mat

foxa2down.Mm.1200.known.mat

wntdown.Hs.1200.known.mat

wntdown.Mm.1200.known.mat

pvalue-topnovelJM (.xls or .txt)

3) Known motifs download all files

foxa2down.Hs.1200.known.mat

foxa2down.Mm.1200.known.mat

wntdown.Hs.1200.known.mat

wntdown.Mm.1200.known.mat

4) Motif comparisons - download all files

(folder)known motifs

motifs compared:

foxa2down.1200.Mm.Hs.cutoff.xls

wntdown.1200.Mm.Hs.cutoff.xls

results:

raw.foxa2down.1200.Mm.Hs.known.tab

raw.wntdown.1200.Mm.Hs.known.tab

significance.xls (p-values)

(folder)novel_motifs

motifs that were compared:

foxa2down.Hs.1200.novel3.RE0.3.mat

foxa2down.Mm.1200.novel3.RE0.3.mat

wntdown.Hs.1200.novel3.RE0.3.mat

wntdown.Mm.1200.novel3.RE0.3.mat

(folder) fox-wnt

Mutual matching:

Mm.foxa2.vs.wnt.1200.3.RE0.3.AF0t3align.txt

Mm.wnt.vs.foxa2.1200.3.RE0.3.AF0t3align.txt

foxa2down.Mm.1200.commonWnt.mat

wntdown.Mm.1200.commonFox.mat

fox.vs.wnt1200-mutual-match-results.txt

(folder) comparison to TRANSFAC

fox.Mm.1200.commonwnt.9.1.AFh2t3alignout.txt

wnt.Mm.1200.commonfox.9.1.AFh2t3alignout.txt

(folder) human-mouse

(Folder) Fox_fg

Mutual matching

Foxa2down.1200.3.RE0.3.Hs.vs.Mm.AF0t3align.txt

Foxa2down.1200.3.RE0.3.Mm.vs.Hs.AF0t3align.txt

Fox1200.Hs.common.Mm-top.txt

Fox1200.Mm.commontoHs-all.txt

mm.vs.hs.Fox1200-mutual-match.results.txt

(folder) comparison to TRANSFAC

Fox1200Hs.common.MmccAFh0t3alignout

Fox1200Hs.common.MmccAFh1t3alignout

Fox1200Hs.common.MmccAFh2t3alignout

(folder)Wnt_fg

Mutual matching

Wntdown.Hs.vs.Mm.1200alignout

Wntdown.Hs.vs.Mm.doc

Wntdown.Mm.vs.Hs.1200alignout

Wntdown.Mm.vs.Hs.doc

Wnt-hm-mm-comparative.doc

(folder) comparison to TRANSFAC

Wnt.Hs.comparedTRANSFAC.doc

Significance of R.E. for human-mouse conserved motifs

pvalue-conservednovelJM.txt

5) novel_motifs_compared_toTRANSFAC download all files

(folder) foxa2downHs1200ccAFalign files

(folder) foxa2downMm1200ccAFalign files

(folder) wntdownHs1200ccAFalign files

(folder) wntdownMm1200ccAFalign files

6) underrepresented motifs download all files

With calculated relative error-rates and sorted

Foxa2down.Mm.1200.switch.mat

Wntdown.Mm.1200.switch.mat

(folder) U-compared to TRANSFAC

7) novel motif discovery by BioProspector download all files

(folder) BPresults-raw

With calculated relative error-rates and sorted

BPfox.Mm.1200.mat

BPwnt.Mm1200.mat

(folder) BP-compared-to-TRANSFAC

(folder) BP-compared-to-DME