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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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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 1513 to 1562 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Divided 224.434 235.583 1.04968
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Subtracted 224.244 234.511 10.267
758 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Divided 224.434 235.583 1.04968
759 bomapin (protease inhibitor 10) (serpin b10). [swissprot;acc:p48595] Subtracted 224.244 234.511 10.267
osteoclast stimulating factor 1. [swissprot;acc:q92882] Divided 231.809 243.289 1.04952
760 plasminogen activator inhibitor-2 precursor (pai-2) (placental plasminogen activator inhibitor) (monocyte arg-serpin) (urokinase inhibitor). [swissprot;acc:p05120] Subtracted 224.244 234.511 10.267
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Divided 246.055 234.458 1.04946
761 serpin b11. [swissprot;acc:q96p15] Subtracted 224.244 234.511 10.267
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Divided 213.325 203.303 1.0493
762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 213.256 203.237
placental thrombin inhibitor (cytoplasmic antiproteinase) (cap) (protease inhibitor 6) (pi-6). [swissprot;acc:p35237] Subtracted 224.244 234.511 10.267
763 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Divided 228.78 218.091 1.04901
764 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] Subtracted 224.244 234.511 10.267
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Divided 222.082 211.707 1.04901
765 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Subtracted 243.067 232.805 10.262
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided 229.045 218.343 1.04901
766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 213.804 224.226 1.04875
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Subtracted 209.191 219.332 10.141
767 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 228.563 238.668 10.105
rho interacting protein 3. [refseq;acc:nm_015134] Divided 213.803 224.224 1.04874
768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] 210.946 221.225 1.04873
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Subtracted 213.325 203.303 10.022
769 cab2. [refseq;acc:nm_033419] Divided 210.946 221.225 1.04873
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Subtracted 213.256 203.237 10.019
770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Divided 210.946 221.225 1.04873
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted 59 49 10
771 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Divided 210.946 221.225 1.04873
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Subtracted 59 49 10
772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Divided 210.946 221.225 1.04873
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Subtracted 59 49 10
773 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Divided 210.946 221.225 1.04873
774 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] Subtracted 221.716 231.501 9.785
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Divided 225.996 215.535 1.04854
775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] 226.003 215.541
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] Subtracted 221.676 231.453 9.777
776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Divided 225.996 215.535 1.04854
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Subtracted 221.965 212.404 9.561
777 histone deacetylase 1 (hd1). [swissprot;acc:q13547] Divided 225.989 215.53 1.04853
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Subtracted 221.965 212.404 9.561
778 beta-catenin (pro2286). [swissprot;acc:p35222] 224.445 214.894 9.551
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] Divided 209.191 219.332 1.04848
779 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] 230.516 241.641 1.04826
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Subtracted 231.734 222.222 9.512
780 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] Divided 232.762 243.933 1.04799
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Subtracted 231.734 222.222 9.512
781 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Divided 245.84 257.636 1.04798

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/