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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2475 to 2524 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
619 Squared coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] 51527.6 43689.1 1.17942
Rooted dendritic cell protein. [refseq;acc:nm_006360] 63.847 68.8873 1.07894
620 Measured ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
Ranked gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 214.256 202.14 1.05994
Squared homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 32208.8 37986.6 1.17939
Rooted potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 63.847 68.8873 1.07894
621 Measured 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 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 214.256 202.14 1.05994
Squared 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 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 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 6228.42 7013.21 1.126
Ranked gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 214.256 202.14 1.05994
Squared gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 32192.5 37966.8 1.17937
Rooted cpz gene product. [refseq;acc:nm_003652] 63.847 68.8873 1.07894
623 Measured cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 6228.39 7013.19 1.126
Ranked gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 214.256 202.14 1.05994
Squared similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 32193.3 37967.7 1.17937
Rooted 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 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 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 32192.5 37966.8 1.17937
Rooted potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 63.847 68.8873 1.07894
625 Measured 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 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 214.256 202.14 1.05994
Squared gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 32192.6 37966.9 1.17937
Rooted 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 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] 6228.39 7013.19 1.126
Ranked gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 214.256 202.14 1.05994
Squared gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] 32192.8 37967.1 1.17937
Rooted probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 59.6673 64.3742 1.07889
627 Measured limkain b1. [refseq;acc:nm_019081] 6228.39 7013.19 1.126
Ranked phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] 214.256 202.139 1.05994
Squared gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] 32192.8 37967.1 1.17937
Rooted probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] 59.6674 64.3747 1.07889
628 Measured putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 6228.39 7013.19 1.126
Ranked gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] 214.256 202.14 1.05994
Squared gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] 32192.6 37966.9 1.17937
Rooted serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] 59.6661 64.3692 1.07882
629 Measured cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] 6228.39 7013.19 1.126
Ranked gamma-aminobutyric-acid receptor alpha-3 subunit precursor (gaba(a) receptor). [swissprot;acc:p34903] 214.256 202.14 1.05994
Squared interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 32192.5 37966.8 1.17937
Rooted synapsin iii. [swissprot;acc:o14994] 60.0129 64.7371 1.07872
630 Measured 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 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 gamma-aminobutyric-acid receptor alpha-4 subunit precursor (gaba(a) receptor). [swissprot;acc:p48169] 32192.8 37967.1 1.17937
Rooted 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 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] 6228.39 7013.19 1.126
Ranked similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] 214.256 202.141 1.05993
Squared gamma-aminobutyric-acid receptor epsilon subunit precursor (gaba(a) receptor). [swissprot;acc:p78334] 32192.8 37967.1 1.17937
Rooted 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

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/