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 2462 to 2511 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
616 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Squared 51527.6 43689.1 1.17942
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Ranked 214.257 202.132 1.05999
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Rooted 57.2007 61.7615 1.07973
617 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Squared 51527.6 43689.1 1.17942
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Measured 5162.52 5822.47 1.12783
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Rooted 57.2008 61.7614 1.07973
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Ranked 214.257 202.135 1.05997
618 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Rooted 57.208 61.7592 1.07956
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Measured 7878.27 8879.08 1.12703
peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Squared 51527.6 43689.1 1.17942
619 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299]
dendritic cell protein. [refseq;acc:nm_006360] Rooted 63.847 68.8873 1.07894
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Ranked 214.256 202.139 1.05994
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Measured 3879.99 4371.24 1.12661
620 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Ranked 214.256 202.14 1.05994
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Squared 32208.8 37986.6 1.17939
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Rooted 63.847 68.8873 1.07894
621 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]
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
622 cpz gene product. [refseq;acc:nm_003652] Rooted 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
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Measured 6228.42 7013.21 1.126
623 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Rooted 63.847 68.8873 1.07894
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Measured 6228.39 7013.19 1.126
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Ranked 214.256 202.14 1.05994
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Squared 32193.3 37967.7 1.17937
624 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Measured 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
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Ranked 214.256 202.139 1.05994
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Rooted 63.847 68.8873 1.07894
625 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 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
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] Rooted 59.6678 64.3767 1.07892
626 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869] Squared 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
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Rooted 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
627 gamma-aminobutyric-acid receptor alpha-6 subunit precursor (gaba(a) receptor). [swissprot;acc:q16445] Squared 32192.8 37967.1 1.17937
limkain b1. [refseq;acc:nm_019081] Measured 6228.39 7013.19 1.126
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Ranked 214.256 202.139 1.05994
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Rooted 59.6674 64.3747 1.07889
628 gamma-aminobutyric-acid receptor alpha-1 subunit precursor (gaba(a) receptor). [swissprot;acc:p14867] Ranked 214.256 202.14 1.05994
gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507] Squared 32192.6 37966.9 1.17937
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] 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/