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.


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Gene Rank Network Comparison Type Value Type description Interaction Map green Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 1 to 50 of 29840 in total
Interaction Map  : High confidence
Rank
Network Comparison Type
Value Type
description
green
Filtered
network_comparison
red
1 Divided Measured mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 0 36400000 364
rad50-interacting protein 1. [refseq;acc:nm_021930] 2394.5 1 5.31521 450.5
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 0 3.70633 4294
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 24 1 2.4 10
Squared cab2. [refseq;acc:nm_033419] 7.16592 0 716592 0.00001
rad50-interacting protein 1. [refseq;acc:nm_021930] 1357.07 1 28.2513 48.0356
Rooted mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0.00001 0 1907880 19.0788
rad50-interacting protein 1. [refseq;acc:nm_021930] 48.9336 1 2.30547 21.225
Subtracted Measured ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 6410 0 6325 85
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] 33356.5 1 8126 41482.5
Ranked homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 322 107 215
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 21883 0 12977 8906
Squared nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 160184 72283 232467
putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 322755 1 145743 468498
Rooted ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] 60.0707 0 50.8706 9.20014
rad50-interacting protein 1. [refseq;acc:nm_021930] 48.9336 1 27.7086 21.225
2 Divided Measured cab2. [refseq;acc:nm_033419] 174 0 17400000 0.00001
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 2394.5 1 5.31521 450.5
Ranked 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] 28 1.86667 15
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] 14977 0 2.55362 5865
Squared nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0.00001 561325 5.61325
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1357.07 1 28.2513 48.0356
Rooted nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 0.00001 0 1240970 12.4097
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 48.9336 1 2.30547 21.225
Subtracted Measured cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 33356.5 8126 41482.5
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 6410 0 6325 85
Ranked adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 15915 11621 4294
hbs1-like. [refseq;acc:nm_006620] 322 1 107 215
Squared histone h4. [swissprot;acc:p02304] 345123 0 71500 273623
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] 263351 1 143938 407289
Rooted lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 60.0707 0 50.8706 9.20014
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 48.9336 1 27.7086 21.225
3 Divided Measured homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 698.5 3.71868 2597.5
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 109 0 10900000 0.00001
Ranked cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 28 1 1.86667 15
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 11083.9 0 2.47638 4475.84
Squared homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 115.48 1 13.8285 1596.92
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0.00001 0 561325 5.61325
Rooted homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 26.4292 1 1.92839 50.9657
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0.00001 0 1240970 12.4097
Subtracted Measured cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 33356.5 1 8126 41482.5
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] 19621.3 0 4196.8 23818.1
Ranked cab2. [refseq;acc:nm_033419] 10950 10916 21866
rad50-interacting protein 1. [refseq;acc:nm_021930] 232 1 105 337
Squared apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 170628 0 35348 135280
cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438] 263351 1 143938 407289
Rooted adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] 6.85565 0 30.0631 36.9188
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] 26.4292 1 24.5365 50.9657
4 Divided Measured hbs1-like. [refseq;acc:nm_006620] 698.5 3.71868 2597.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 89 0 8900000 0.00001

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/