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 1413 to 1462 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
707 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Subtracted 220.438 209.118 11.32
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Divided 1.05413
708 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Subtracted 11.32
709 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Divided 1.05413
710 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Subtracted 220.437 11.319
711 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 220.431 209.123 11.308
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Divided 232.468 245.048 1.05411
712 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Subtracted 232.762 243.933 11.171
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided 220.431 209.123 1.05407
713 dendritic cell protein. [refseq;acc:nm_006360] 223.121 211.685 1.05402
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Subtracted 224.434 235.583 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 223.121 211.685 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 224.434 235.583 11.149
716 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
cpz gene product. [refseq;acc:nm_003652] Divided 223.121 211.685 1.05402
717 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Subtracted 224.434 235.583 11.149
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Divided 223.121 211.685 1.05402
718 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Subtracted 224.434 235.583 11.149
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Divided 223.121 211.685 1.05402
719 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Subtracted 230.516 241.641 11.125
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Divided 247.769 235.074 1.054
720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 231.92 244.435 1.05396
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Subtracted 217.952 206.902 11.05
721 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] Divided 214.765 203.8 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] 244.447 233.508 10.939
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] Divided 217.952 206.902 1.05341
723 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 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 244.447 233.508 10.939
724 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided 244.842 232.577 1.05274
down-regulated in metastasis. [refseq;acc:nm_014503] Subtracted 244.447 233.508 10.939
725 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Divided 235.296 247.673 1.0526
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] Subtracted 214.679 225.568 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 244.495 232.419 1.05196
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 222.825 211.966 10.859
727 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Divided 208.873 219.71 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 208.874 219.708 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

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/