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 486 to 535 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
61 necdin. [swissprot;acc:q99608] Squared 1 219048 129762 1.68808
testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562] Ranked 0 15352 11346.5 1.35302
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] Rooted 6.63325 4.58258 1.44749
62 bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] 15.0883 21.8314 1.44691
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Measured 210.767 384.407 1.82385
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Squared 21.2079 6.15501 3.44563
glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311] Ranked 9418.7 12695.6 1.34791
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Measured 1 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Ranked 266.865 336.181 1.25974
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Squared 219048 129762 1.68808
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Rooted 43.4519 31.7522 1.36847
63 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 0 18.1049 12.6095 1.43581
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Ranked 1 266.865 336.178 1.25973
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] Rooted 43.4554 31.7576 1.36835
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Squared 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Measured 4489.19 2765.82 1.6231
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 0 8519.83 11453 1.34428
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Squared 1.24091 0.365145 3.3984
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Measured 31.1429 56.278 1.80709
64 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Rooted 1 63.8686 47.2654 1.35128
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] Measured 4489.19 2765.82 1.6231
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-11 subunit. [swissprot;acc:p50152] Ranked 266.868 336.159 1.25965
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Squared 219048 129762 1.68808
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Rooted 0 15.7225 22.5496 1.43422
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 18 1800000
similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517] Ranked 15264 20387 1.33563
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Squared 50.8715 15.2519 3.33542
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 15.1833 3.33538
60s ribosomal protein l21. [swissprot;acc:p46778] Rooted 20.5734 29.2291 1.42072
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Ranked 7853.67 10406.3 1.32502
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Rooted 1 63.8686 47.2654 1.35128
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Ranked 267.136 336.077 1.25807
melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Squared 219048 129762 1.68808
neuralized-like. [refseq;acc:nm_004210] Measured 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 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared 1797.76 558.241 3.2204
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Rooted 1 63.8686 47.2654 1.35128
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Ranked 267.136 336.077 1.25807
heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] 0 11461 15180 1.32449
melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362] Squared 1 219048 129762 1.68808
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 3221.38 1.61795
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Rooted 0 30.9855 21.9983 1.40854
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Measured 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
Squared 608.191 190.865 3.1865
guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Ranked 1 267.14 336.075 1.25805
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Rooted 0 11.0051 15.3166 1.39177
melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361] Squared 1 219048 129762 1.68808
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Rooted 63.8686 47.2654 1.35128

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/