MK5 Microarray Data

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 1663 to 1712 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
1663	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494]	7433.73	7950.61	1.06953
1664	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]
1665	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	5791.14	6193.02	1.0694
1666	fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469]
1667	fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540]
1668	wd-repeat protein 4. [swissprot;acc:p57081]
1669	myelin p2 protein. [swissprot;acc:p02689]
1670	kelch-like protein 8. [swissprot;acc:q9p2g9]
1671	phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086]
1672	beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]
1673	beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429]
1674	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]
1675	retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329]
1676	indolethylamine n-methyltransferase (ec 2.1.1.49) (aromatic alkylamine n-methyltransferase) (indolamine n-methyltransferase) (arylamine n- methyltransferase) (amine n-methyltransferase). [swissprot;acc:o95050]
1677	ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792]	6075.19	6496.61	1.06937
1678	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]	5763.25	6162.98	1.06936
1679	proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720]	6180.24	6608.11	1.06923
1680	methylenetetrahydrofolate reductase (ec 1.5.1.20). [swissprot;acc:p42898]	6436.73	6882.16	1.0692
1681	f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2]	6304.74	6740.66	1.06914
1682	f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756]
1683	ring finger protein 20. [refseq;acc:nm_019592]	5419.54	5793.94	1.06908
1684	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]
1685	gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6]	6088.07	6508.45	1.06905
1686	toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]
1687	serpin b12. [swissprot;acc:q96p63]	5767.69	6165.87	1.06904
1688	megsin (tp55) (serpin b7). [swissprot;acc:o75635]
1689	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
1690	oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055]
1691	upf0183 protein. [swissprot;acc:q9bsu1]
1692	antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
1693	translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232]
1694	squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508]
1695	oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133]
1696	wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5]	6304.22	6738.77	1.06893
1697	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	6304.21
1698	wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558]	6304.22
1699	rest corepressor. [refseq;acc:nm_015156]	6304.21
1700	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747]	6326.24	6762.27	1.06892
1701	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]
1702	dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]
1703	phosphoinositide-3-kinase, class 2, alpha polypeptide; c2-containing phosphatidylinositol kinase. [refseq;acc:nm_002645]
1704	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	5778.4	6176.13	1.06883
1705	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	5369.43	5738.73	1.06878
1706	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]
1707	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	5777.1	6174.15	1.06873
1708	metaxin 2. [swissprot;acc:o75431]	7033.72	7516.77	1.06868
1709	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	5775.55	6171.79	1.06861
1710	camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861]	5916.13	6321.77	1.06857
1711	protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817]	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

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.