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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4958 to 5007 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
620 microtubule-associated protein 4 (map 4). [swissprot;acc:p27816] Ranked Subtracted 206.274 218.792 12.518
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Rooted Divided 63.847 68.8873 1.07894
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Squared Subtracted 27407.7 31927.7 4520
621 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Ranked 231.92 244.435 12.515
actin binding lim protein 2. [refseq;acc:nm_032432] Rooted 60.0129 64.7371 4.7242
calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746] Squared 27407.7 31927.7 4520
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Rooted Divided 63.847 68.8873 1.07894
ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Measured 4115.39 4633.96 1.12601
gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Ranked 214.256 202.14 1.05994
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Squared 32193.3 37967.7 1.17937
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Measured Subtracted 6805.86 7540.99 735.13
622 cpz gene product. [refseq;acc:nm_003652] Rooted Divided 63.847 68.8873 1.07894
gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Ranked 214.256 202.14 1.05994
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Squared 32192.5 37966.8 1.17937
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Rooted Subtracted 60.0129 64.7371 4.7242
melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Squared 27407.7 31927.7 4520
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Measured Divided 6228.42 7013.21 1.126
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Subtracted 6805.45 7540.5 735.05
synapsin iii. [swissprot;acc:o14994] Ranked 229.072 216.576 12.496
623 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Squared 27407.7 31927.7 4520
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Ranked 229.072 216.576 12.496
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Rooted Divided 63.847 68.8873 1.07894
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Measured 6228.39 7013.19 1.126
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Subtracted 4490.28 5222.25 731.97
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Ranked Divided 214.256 202.14 1.05994
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Squared 32193.3 37967.7 1.17937
synapsin ii. [swissprot;acc:q92777] Rooted Subtracted 60.0129 64.7371 4.7242
624 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured 4490.28 5222.25 731.97
calcium-binding mitochondrial carrier protein aralar2 (solute carrier family 25, member 13) (citrin). [swissprot;acc:q9ujs0] Squared 27407.7 31927.7 4520
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Measured Divided 6228.39 7013.19 1.126
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Squared 32192.5 37966.8 1.17937
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Ranked Subtracted 229.072 216.576 12.496
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Divided 214.256 202.139 1.05994
mitochondrial ribosome recycling factor. [refseq;acc:nm_138777] Rooted Subtracted 60.0129 64.7371 4.7242
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Divided 63.847 68.8873 1.07894
625 actin binding lim protein 2. [refseq;acc:nm_032432] Ranked Subtracted 229.072 216.576 12.496
acyl carrier protein, mitochondrial precursor (acp) (nadh-ubiquinone oxidoreductase 9.6 kda subunit) (ci-sdap). [swissprot;acc:o14561] Squared 27407.7 31927.7 4520
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Measured Divided 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] Ranked 214.256 202.14 1.05994
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Squared 32192.6 37966.9 1.17937
peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542] Rooted Subtracted 60.0129 64.7371 4.7242
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Divided 59.6678 64.3767 1.07892
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Measured Subtracted 5291.92 6020.19 728.27
626 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Squared Divided 32192.8 37967.1 1.17937
gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] Ranked 214.256 202.14 1.05994
hairy/enhancer-of-split related with yrpw motif 2; gridlock; hes-related repressor protein 1. [refseq;acc:nm_012259] Rooted Subtracted 60.0129 64.7371 4.7242
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Ranked 229.072 216.576 12.496
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared 24560.6 29071.1 4510.5
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Rooted Divided 59.6673 64.3742 1.07889
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Measured 6228.39 7013.19 1.126

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/