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 3401 to 3450 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1701 indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050] Subtracted 5791.14 6193.02 401.88
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Divided 6326.24 6762.27 1.06892
1702 arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [swissprot;acc:p78540] Subtracted 6267.93 6668.72 400.79
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Divided 6326.24 6762.27 1.06892
1703 phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Subtracted 5925.65 6326.43 400.78
1704 homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Divided 5778.4 6176.13 1.06883
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Subtracted 5925.65 6326.43 400.78
1705 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 4057.54 4457.66 400.12
translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144] Divided 5369.43 5738.73 1.06878
1706 arginase 1 (ec 3.5.3.1) (liver-type arginase). [swissprot;acc:p05089] Subtracted 6271.17 6670.97 399.8
translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50] Divided 5369.43 5738.73 1.06878
1707 cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Subtracted 5763.25 6162.98 399.73
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Divided 5777.1 6174.15 1.06873
1708 inositol polyphosphate multikinase. [refseq;acc:nm_152230] Subtracted 5466 5865.33 399.33
metaxin 2. [swissprot;acc:o75431] Divided 7033.72 7516.77 1.06868
1709 afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Subtracted 5466 5865.33 399.33
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Divided 5775.55 6171.79 1.06861
1710 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5] Subtracted 5466 5865.33 399.33
camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] Divided 5916.13 6321.77 1.06857
1711 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] Subtracted 5941.29 6339.93 398.64
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Divided 5917.22 6322.72 1.06853
1712 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 5917.23 6322.73
copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] Subtracted 5941.83 6340.32 398.49
1713 camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] Divided 5917.23 6322.73 1.06853
serpin b12. [swissprot;acc:q96p63] Subtracted 5767.69 6165.87 398.18
1714 camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] Divided 5917.23 6322.73 1.06853
megsin (tp55) (serpin b7). [swissprot;acc:o75635] Subtracted 5767.69 6165.87 398.18
1715 camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] Divided 5918.48 6323.83 1.06849
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Subtracted 5767.69 6165.87 398.18
1716 inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Divided 6070.41 6485.85 1.06844
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Subtracted 5767.69 6165.87 398.18
1717 inositol-1(or 4)-monophosphatase (ec 3.1.3.25) (impase) (imp) (inositol monophosphatase) (lithium-sensitive myo-inositol monophosphatase a1). [swissprot;acc:p29218] Divided 6069.65 6484.94 1.06842
upf0183 protein. [swissprot;acc:q9bsu1] Subtracted 5767.69 6165.87 398.18
1718 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Divided 9720.64 9099.1 1.06831
1719 mannose-6-phosphate isomerase (ec 5.3.1.8) (phosphomannose isomerase) (pmi) (phosphohexomutase). [swissprot;acc:p34949] 5458.12 5830.76 1.06827
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Subtracted 5767.69 6165.87 398.18
1720 putative ankyrin-repeat containing protein. [refseq;acc:nm_025185] Divided 5458.12 5830.76 1.06827
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Subtracted 5767.69 6165.87 398.18
1721 mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Divided 5458.12 5830.76 1.06827
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Subtracted 5767.69 6165.87 398.18
1722 exocyst complex component sec6. [swissprot;acc:o60645] 7387.42 7785.45 398.03
protocadherin fat 2 precursor (hfat2) (multiple epidermal growth factor-like domains 1). [swissprot;acc:q9nyq8] Divided 5458.12 5830.76 1.06827
1723 cadherin-related tumor suppressor homolog precursor (fat protein homolog). [swissprot;acc:q14517]
glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] Subtracted 6215.55 6613.46 397.91
1724 ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 5885.08 6282.97 397.89
mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772] Divided 5458.12 5830.76 1.06827
1725 glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744] 6051.06 6463.65 1.06818
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Subtracted 5778.4 6176.13 397.73

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/