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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Value Type Rank Filtered Gene description green Interaction Map Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 101 to 150 of 14920 in total
Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
Filtered
description
green
network_comparison
red
51 0 ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 88.5622 2.0824 184.422
1 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1390.33 1.78438 779.167
52 0 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 481.725 2.07438 999.28
1 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 1390.33 1.78438 779.167
53 0 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 861.814 2.05016 420.365
1 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 1390.33 1.78438 779.167
54 0 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 330.189 1.93484 638.862
1 deltex 2. [refseq;acc:nm_020892] 2651.88 1.63814 1618.84
55 0 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 327.517 1.92644 630.942
1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 2662.12 1.63399 1629.21
56 0 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 142.981 1.89874 271.484
1 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] 2664.55 1.63302 1631.67
57 0 5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 142.417 1.89769 270.264
1 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 2664.55 1.63302 1631.67
58 0 40s ribosomal protein s26. [swissprot;acc:p02383] 81.2233 1.85588 150.741
1 kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 2664.55 1.63302 1631.67
59 0 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 279.24 1.85328 150.673
1 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 2664.55 1.63302 1631.67
60 0 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 87.5499 1.8441 47.4756
1 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 2765.82 1.6231 4489.19
61 0 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 593.094 1.82804 324.442
1 glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 2765.82 1.6231 4489.19
62 0 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 384.407 1.82385 210.767
1 glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 2765.82 1.6231 4489.19
63 0 spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 56.278 1.80709 31.1429
1 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 2765.82 1.6231 4489.19
64 0 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] 18 1800000 0.00001
1 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 2765.82 1.6231 4489.19
65 0 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0.00001 1800000 18
1 neuralized-like. [refseq;acc:nm_004210] 2690.25 1.6229 1657.68
66 0 soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 385.626 1.78524 688.436
1 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 3221.38 1.61795 1991.03
67 0 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 898 1.78508 1603
1 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 10307.5 1.59177 6475.5
68 0 protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 351.772 1.76802 198.964
1 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 10307.5 1.59177 6475.5
69 0 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 2804 1.7602 1593
1 spermatogenesis associated 6. [refseq;acc:nm_019073] 10307.5 1.59177 6475.5
70 0 importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 1068 1.75947 607
1 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 10307.5 1.59177 6475.5
71 0 ubiquitin protein ligase. [refseq;acc:nm_130466] 352.75 1.75762 620
1 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 2945.26 1.54716 4556.78
72 0 60s ribosomal protein l21. [swissprot;acc:p46778] 992.083 1.73441 572
1 uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 2945.28 1.54715 4556.79
73 0 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 37.693 1.73233 65.2968
1 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 2945.38 1.54711 4556.83
74 0 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 859.34 1.71473 501.151
1 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 2945.8 1.54694 4556.99
75 0 oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 925.298 1.71412 1586.07
1 nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 2907.43 1.5137 1920.75

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/