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 113 to 162 of 3730 in total
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
57 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] 0 270.264 142.417 1.89769
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 1 1631.67 2664.55 1.63302
58 40s ribosomal protein s26. [swissprot;acc:p02383] 0 150.741 81.2233 1.85588
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 1631.67 2664.55 1.63302
59 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] 0 150.673 279.24 1.85328
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 1 1631.67 2664.55 1.63302
60 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 4489.19 2765.82 1.6231
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] 0 47.4756 87.5499 1.8441
61 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 324.442 593.094 1.82804
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 4489.19 2765.82 1.6231
62 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 0 210.767 384.407 1.82385
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 1 4489.19 2765.82 1.6231
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 31.1429 56.278 1.80709
64 glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 4489.19 2765.82 1.6231
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] 0 0.00001 18 1800000
65 neuralized-like. [refseq;acc:nm_004210] 1 1657.68 2690.25 1.6229
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 18 0.00001 1800000
66 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] 1 1991.03 3221.38 1.61795
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 688.436 385.626 1.78524
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 6475.5 10307.5 1.59177
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 1603 898 1.78508
68 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 1 6475.5 10307.5 1.59177
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 0 198.964 351.772 1.76802
69 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 1593 2804 1.7602
spermatogenesis associated 6. [refseq;acc:nm_019073] 1 6475.5 10307.5 1.59177
70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] 0 607 1068 1.75947
71 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] 1 4556.78 2945.26 1.54716
ubiquitin protein ligase. [refseq;acc:nm_130466] 0 620 352.75 1.75762
72 60s ribosomal protein l21. [swissprot;acc:p46778] 572 992.083 1.73441
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] 1 4556.79 2945.28 1.54715
73 protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 65.2968 37.693 1.73233
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] 1 4556.83 2945.38 1.54711
74 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 0 501.151 859.34 1.71473
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] 1 4556.99 2945.8 1.54694
75 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] 1920.75 2907.43 1.5137
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 1586.07 925.298 1.71412
76 dead-box protein. [refseq;acc:nm_018665] 313.667 183 1.71403
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 1 4599.26 3058.57 1.50373
77 inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] 0 712.071 416.524 1.70956
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 1 4612.39 3093.6 1.49095
78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 4800.81 7132.71 1.48573
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 0 161 95 1.69474
79 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] 323.79 544.991 1.68316
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 1 3074.57 4567.51 1.48558
80 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 5945.32 1.43834
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] 0 293 493 1.68259
81 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 4136.36 5943.56 1.43691
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] 0 30 50 1.66667

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/