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 Network Comparison Type Value Type Interaction Map red network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 1451 to 1500 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
726 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] Divided 244.495 1.05196 232.419
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 222.825 10.859 211.966
727 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Divided 208.873 1.05188 219.71
Subtracted 10.837
728 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] Divided 208.874 1.05187 219.708
Subtracted 10.834
729 huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Divided 1.05187
Subtracted 10.834
730 mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] Divided 1.05187
Subtracted 10.834
731 fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Divided 1.05187
Subtracted 10.834
732 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Divided 124.434 1.05169 118.318
translin. [swissprot;acc:q15631] Subtracted 224.385 10.746 235.131
733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Divided 164 1.05154 155.961
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted 224.385 10.746 235.131
734 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Divided 232.601 1.0513 244.534
735 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Subtracted 229.045 10.702 218.343
736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Divided 232.601 1.0513 244.534
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 228.78 10.689 218.091
737 exocyst complex component sec15b. [swissprot;acc:q9y2d4] 221.968 10.642 211.326
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 125.526 1.05129 119.402
738 exocyst complex component sec15a. [swissprot;acc:q8tag9] Subtracted 222.138 10.635 211.503
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Divided 222.825 1.05123 211.966
739 3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530] Subtracted 272.878 10.594 283.472
phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Divided 223.58 1.0512 235.027
740 bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939]
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 223.463 10.588 212.875
741 multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Divided 223.58 1.0512 235.027
step ii splicing factor slu7. [refseq;acc:nm_006425] Subtracted 223.463 10.588 212.875
742 brain protein 44. [swissprot;acc:o95563] Divided 126.215 1.05111 120.078
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Subtracted 226.003 10.462 215.541
743 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 10.461 215.535
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Divided 126.215 1.05111 120.078
744 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Subtracted 225.996 10.461 215.535
septin 6. [swissprot;acc:q14141] Divided 126.604 1.05098 120.463
745 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Subtracted 225.989 10.459 215.53
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Divided 214.679 1.05072 225.568
746 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 250.465 1.0507 238.38
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Subtracted 213.804 10.422 224.226
747 rho interacting protein 3. [refseq;acc:nm_015134] 213.803 10.421 224.224
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 250.465 1.0507 238.38
748 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 245.246 1.05038 233.483
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Subtracted 222.082 10.375 211.707
749 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 10.279 221.225
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Divided 221.968 1.05036 211.326
750 cab2. [refseq;acc:nm_033419] Subtracted 210.946 10.279 221.225
exocyst complex component sec15a. [swissprot;acc:q8tag9] Divided 222.138 1.05028 211.503

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/