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