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 Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2480 to 2529 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
620 Rooted CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 63.847 68.8873 1.07894
621 Measured FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 4115.39 4633.96 1.12601
Ranked GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 214.256 202.14 1.05994
Squared NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 32193.3 37967.7 1.17937
Rooted CPN1 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] 63.847 68.8873 1.07894
622 Measured FTMT mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 6228.42 7013.21 1.126
Ranked GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 214.256 202.14 1.05994
Squared GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 32192.5 37966.8 1.17937
Rooted CPZ cpz gene product. [refseq;acc:nm_003652] 63.847 68.8873 1.07894
623 Measured CREG2 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 6228.39 7013.19 1.126
Ranked GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 214.256 202.14 1.05994
Squared PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 32193.3 37967.7 1.17937
Rooted CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 63.847 68.8873 1.07894
624 Measured no value dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 6228.39 7013.19 1.126
Ranked interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 214.256 202.139 1.05994
Squared FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 32192.5 37966.8 1.17937
Rooted CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 63.847 68.8873 1.07894
625 Measured DLGAP1 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] 6228.39 7013.19 1.126
Ranked GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 214.256 202.14 1.05994
Squared GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 32192.6 37966.9 1.17937
Rooted HTRA2 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] 59.6678 64.3767 1.07892
626 Measured AHCYL1 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 6228.39 7013.19 1.126
Ranked GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 214.256 202.14 1.05994
Squared GABRA2 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 32192.8 37967.1 1.17937
Rooted HTRA3 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 59.6673 64.3742 1.07889
627 Measured KIAA0430 limkain b1. [refseq;acc:nm_019081] 6228.39 7013.19 1.126
Ranked JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 214.256 202.139 1.05994
Squared GABRA6 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 32192.8 37967.1 1.17937
Rooted HTRA4 probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 59.6674 64.3747 1.07889
628 Measured no value putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 6228.39 7013.19 1.126
Ranked GABRA1 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 214.256 202.14 1.05994
Squared GABRG2 gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 32192.6 37966.9 1.17937
Rooted HTRA1 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 59.6661 64.3692 1.07882
629 Measured CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 6228.39 7013.19 1.126
Ranked GABRA3 gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
Squared no value interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 32192.5 37966.8 1.17937
Rooted SYN3 synapsin iii. [swissprot;acc:o14994] 60.0129 64.7371 1.07872
630 Measured DLGAP3 disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] 6228.39 7013.19 1.126
Ranked NDUFA6 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] 214.256 202.141 1.05993
Squared GABRA4 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 32192.8 37967.1 1.17937
Rooted no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] 60.0129 64.7371 1.07872
631 Measured KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 6228.39 7013.19 1.126
Ranked PDXDC1 similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
Squared GABRE gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 32192.8 37967.1 1.17937
Rooted HEY1 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] 60.0129 64.7371 1.07872
632 Measured no value disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 6228.39 7013.19 1.126
Ranked HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 214.254 202.166 1.05979
Squared JMJD6 phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 32192.5 37966.8 1.17937
Rooted ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] 60.0129 64.7371 1.07872
633 Measured FTL ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 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
- Hugo is the HGNC identifier if it exists
- 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/