Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Filtered Value Type description Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total
Rank
Filtered
Value Type
description
Network Comparison Type
Interaction Map
green
red
network_comparison
1 0 Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted High confidence 6410 85 6325
Low confidence
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided High confidence 0.00001 364 36400000
Low confidence
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 15915 4294 3.70633
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 21883 8906 12977
Low confidence
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 14977 5865 2.55362
Squared cab2. [refseq;acc:nm_033419] High confidence 7.16592 0.00001 716592
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 1.87479 187479
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted High confidence 160184 232467 72283
Low confidence
Rooted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] High confidence 60.0707 9.20014 50.8706
Low confidence
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided High confidence 0.00001 19.0788 1907880
Low confidence
1 Measured carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted 32028.5 40899 8870.5
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided 543.5 2399.5 4.4149
mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476] Subtracted High confidence 33356.5 41482.5 8126
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 2394.5 450.5 5.31521
Ranked carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 32 16 2
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Subtracted High confidence 322 215 107
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 330 223
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Divided High confidence 24 10 2.4
Squared carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Subtracted Low confidence 242799 395912 153113
lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Divided 69.9153 1362.75 19.4914
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Subtracted High confidence 322755 468498 145743
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided 1357.07 48.0356 28.2513
Rooted lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [swissprot;acc:p11279] Low confidence 23.3131 48.9847 2.10117
Subtracted 25.6716
rad50-interacting protein 1. [refseq;acc:nm_021930] Divided High confidence 48.9336 21.225 2.30547
Subtracted 27.7086
2 0 Measured cab2. [refseq;acc:nm_033419] Divided 174 0.00001 17400000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Low confidence 89 8900000
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted High confidence 6410 85 6325
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Low confidence 19621.3 23818.1 4196.8
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] High confidence 15915 4294 11621
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Divided Low confidence 21883 8906 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 14977 5865 2.55362
neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531] Subtracted Low confidence 20617 9607 11010
Squared histone h4. [swissprot;acc:p02304] High confidence 345123 273623 71500
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided Low confidence 1.87479 0.00001 187479
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] High confidence 0.00001 5.61325 561325
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Subtracted Low confidence 386144 414704 28560
Rooted homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 9.43398 0.00001 943398
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted High confidence 60.0707 9.20014 50.8706
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Low confidence 7.61577 29.3087 21.6929
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Divided High confidence 0.00001 12.4097 1240970
1 Measured 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted Low confidence 28492 21185 7307
cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [swissprot;acc:p11802] Divided 543.5 2399.5 4.4149

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/