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 Interaction Map Value Type Filtered network_comparison red green Network Comparison Type
Results: HTML CSV LaTeX Showing element 501 to 550 of 14920 in total
Interaction Map  : High confidence
Network Comparison Type  : Divided
Rank
description
Value Type
Filtered
network_comparison
red
green
63 myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 1 1.6231 4489.19 2765.82
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 0 1.34428 8519.83 11453
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 3.3984 1.24091 0.365145
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Measured 1.80709 31.1429 56.278
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 1 1.35128 63.8686 47.2654
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured 1.6231 4489.19 2765.82
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 1.25965 266.868 336.159
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 1.68808 219048 129762
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Rooted 0 1.43422 15.7225 22.5496
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] Measured 1800000 0.00001 18
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Ranked 1.33563 15264 20387
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Squared 3.33542 50.8715 15.2519
65 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] 3.33538 50.642 15.1833
60s ribosomal protein l21. [swissprot;acc:p46778] Rooted 1.42072 20.5734 29.2291
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Ranked 1.32502 7853.67 10406.3
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 1 1.35128 63.8686 47.2654
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 1.25807 267.136 336.077
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 1.68808 219048 129762
neuralized-like. [refseq;acc:nm_004210] Measured 1.6229 1657.68 2690.25
rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 1800000 18 0.00001
66 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 3.2204 1797.76 558.241
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted 1 1.35128 63.8686 47.2654
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 1.25807 267.136 336.077
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 1.32449 11461 15180
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 1 1.68808 219048 129762
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] Measured 1.61795 1991.03 3221.38
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 0 1.40854 30.9855 21.9983
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 1.78524 688.436 385.626
67 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 1 1.59177 6475.5 10307.5
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 0 1.78508 1603 898
Squared 3.1865 608.191 190.865
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked 1 1.25805 267.14 336.075
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Rooted 0 1.39177 11.0051 15.3166
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 1 1.68808 219048 129762
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 1.35128 63.8686 47.2654
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] Ranked 0 1.32408 10793.5 14291.5
68 alpha crystallin a chain. [swissprot;acc:p02489] Rooted 1.38766 6.22183 8.63381
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Measured 1 1.59177 6475.5 10307.5
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Rooted 1.35128 63.8686 47.2654
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Ranked 1.25805 267.139 336.075
melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732] Squared 1.68808 219048 129762
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 3136000 31.36 0.00001
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Measured 1.76802 198.964 351.772
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Ranked 1.32362 8932.56 11823.3
69 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Rooted 1.38596 18.7392 13.5207
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Ranked 1.32051 7704.7 10174.1
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Measured 1.7602 1593 2804
guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Ranked 1 1.25805 267.14 336.075
melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Squared 1.68808 219048 129762
neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Rooted 1.33581 27.9136 37.2872

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/