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 Value Type Gene description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Value Type
description
Filtered
red
green
network_comparison
63 Squared melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 1 219048 129762 1.68808
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 1.24091 0.365145 3.3984
Rooted dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 18.1049 12.6095 1.43581
kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] 1 43.4554 31.7576 1.36835
64 Measured glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 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
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] 1 266.868 336.159 1.25965
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] 0 15264 20387 1.33563
Squared melanoma antigen, family b, 6. [refseq;acc:nm_173523] 1 219048 129762 1.68808
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 0 50.8715 15.2519 3.33542
Rooted 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 1 63.8686 47.2654 1.35128
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 0 15.7225 22.5496 1.43422
65 Measured 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
Ranked e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] 7853.67 10406.3 1.32502
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 1 267.136 336.077 1.25807
Squared 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 50.642 15.1833 3.33538
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] 1 219048 129762 1.68808
Rooted 60s ribosomal protein l21. [swissprot;acc:p46778] 0 20.5734 29.2291 1.42072
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 1 63.8686 47.2654 1.35128
66 Measured 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] 1991.03 3221.38 1.61795
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 688.436 385.626 1.78524
Ranked guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] 1 267.136 336.077 1.25807
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 11461 15180 1.32449
Squared dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 1797.76 558.241 3.2204
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] 1 219048 129762 1.68808
Rooted glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 63.8686 47.2654 1.35128
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 30.9855 21.9983 1.40854
67 Measured 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
Ranked guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] 1 267.14 336.075 1.25805
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 0 10793.5 14291.5 1.32408
Squared filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 608.191 190.865 3.1865
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] 1 219048 129762 1.68808
Rooted isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 11.0051 15.3166 1.39177
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] 1 63.8686 47.2654 1.35128
68 Measured beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] 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
Ranked guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] 1 267.139 336.075 1.25805
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] 0 8932.56 11823.3 1.32362
Squared melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] 1 219048 129762 1.68808
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 31.36 0.00001 3136000
Rooted alpha crystallin a chain. [swissprot;acc:p02489] 6.22183 8.63381 1.38766
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 63.8686 47.2654 1.35128
69 Measured dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 0 1593 2804 1.7602
spermatogenesis associated 6. [refseq;acc:nm_019073] 1 6475.5 10307.5 1.59177
Ranked collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] 0 7704.7 10174.1 1.32051
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] 1 267.14 336.075 1.25805
Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] 219048 129762 1.68808
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] 0 16.2406 50.7408 3.12432

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/