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 3364 to 3413 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1682 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Divided 6304.74 6740.66 1.06914
1683 leng5 protein. [refseq;acc:nm_024075] Subtracted 5372.25 5775.21 402.96
ring finger protein 20. [refseq;acc:nm_019592] Divided 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]
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Subtracted 5372.25 5775.21 402.96
1685 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Divided 6088.07 6508.45 1.06905
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Subtracted 5372.25 5775.21 402.96
1686 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603] Divided 6088.07 6508.45 1.06905
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Subtracted 5372.25 5775.21 402.96
1687 serpin b12. [swissprot;acc:q96p63] Divided 5767.69 6165.87 1.06904
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted 5372.25 5775.21 402.96
1688 megsin (tp55) (serpin b7). [swissprot;acc:o75635] Divided 5767.69 6165.87 1.06904
transcription factor iib. [refseq;acc:nm_013242] Subtracted 9146.11 8743.98 402.13
1689 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided 5767.69 6165.87 1.06904
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Subtracted 9146.11 8743.98 402.13
1690 fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] 5791.14 6193.02 401.88
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [swissprot;acc:p55055] Divided 5767.69 6165.87 1.06904
1691 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Subtracted 5791.14 6193.02 401.88
upf0183 protein. [swissprot;acc:q9bsu1] Divided 5767.69 6165.87 1.06904
1692 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Subtracted 5791.14 6193.02 401.88
1693 translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Divided 5767.69 6165.87 1.06904
wd-repeat protein 4. [swissprot;acc:p57081] Subtracted 5791.14 6193.02 401.88
1694 myelin p2 protein. [swissprot;acc:p02689]
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Divided 5767.69 6165.87 1.06904
1695 kelch-like protein 8. [swissprot;acc:q9p2g9] Subtracted 5791.14 6193.02 401.88
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Divided 5767.69 6165.87 1.06904
1696 phenylethanolamine n-methyltransferase (ec 2.1.1.28) (pnmtase) (noradrenaline n-methyltransferase). [swissprot;acc:p11086] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Divided 6304.22 6738.77 1.06893
1697 beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Divided 6304.21 6738.77 1.06893
1698 beta-carotene 15, 15'-dioxygenase; beta-carotene 15,15'-monooxygenase. [refseq;acc:nm_017429] Subtracted 5791.14 6193.02 401.88
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Divided 6304.22 6738.77 1.06893
1699 fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Subtracted 5791.14 6193.02 401.88
rest corepressor. [refseq;acc:nm_015156] Divided 6304.21 6738.77 1.06893
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
retinal pigment epithelium-specific protein 65kda; retinal pigment epithelium-specific protein (65kd); retinitis pigmentosa 20 (autosomal recessive). [refseq;acc:nm_000329] Subtracted 5791.14 6193.02 401.88
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]
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

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/