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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Network Comparison Type Value Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 1425 to 1474 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
713 dendritic cell protein. [refseq;acc:nm_006360] Divided 211.685 223.121 1.05402
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Subtracted 235.583 224.434 11.149
714 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005]
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Divided 211.685 223.121 1.05402
715 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Subtracted 235.583 224.434 11.149
716 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
cpz gene product. [refseq;acc:nm_003652] Divided 211.685 223.121 1.05402
717 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Subtracted 235.583 224.434 11.149
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Divided 211.685 223.121 1.05402
718 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Subtracted 235.583 224.434 11.149
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Divided 211.685 223.121 1.05402
719 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Subtracted 241.641 230.516 11.125
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Divided 235.074 247.769 1.054
720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 244.435 231.92 1.05396
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Subtracted 206.902 217.952 11.05
721 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Divided 203.8 214.765 1.0538
Subtracted 10.965
722 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] 233.508 244.447 10.939
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Divided 206.902 217.952 1.05341
723 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 232.577 244.842 1.05274
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] Subtracted 233.508 244.447 10.939
724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided 232.577 244.842 1.05274
down-regulated in metastasis. [refseq;acc:nm_014503] Subtracted 233.508 244.447 10.939
725 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Divided 247.673 235.296 1.0526
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Subtracted 225.568 214.679 10.889
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 232.419 244.495 1.05196
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 211.966 222.825 10.859
727 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Divided 219.71 208.873 1.05188
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 219.708 208.874 1.05187
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 118.318 124.434 1.05169
translin. [swissprot;acc:q15631] Subtracted 235.131 224.385 10.746
733 acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] Divided 155.961 164 1.05154
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted 235.131 224.385 10.746
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 244.534 232.601 1.0513
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 218.343 229.045 10.702
736 presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] Divided 244.534 232.601 1.0513
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Subtracted 218.091 228.78 10.689
737 exocyst complex component sec15b. [swissprot;acc:q9y2d4] 211.326 221.968 10.642
septin 10 isoform 1. [refseq;acc:nm_144710] Divided 119.402 125.526 1.05129

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/