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 3977 to 4026 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1989 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Divided 219.261 217.195 1.00951
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Subtracted 217.662 215.693 1.969
1990 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 219.26 217.194 1.00951
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Subtracted 217.676 215.709 1.967
1991 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 217.941 215.979 1.962
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Divided 219.26 217.194 1.00951
1992 proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Subtracted 216.201 214.245 1.956
zasp protein (fragment). [sptrembl;acc:q9y4z3] Divided 219.267 217.207 1.00948
1993 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Subtracted 198.3 196.347 1.953
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Divided 189.052 190.835 1.00943
1994 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Subtracted 198.293 196.341 1.952
goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Divided 189.011 190.787 1.0094
1995 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 188.961 190.73 1.00936
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Subtracted 198.258 196.319 1.939
1996 prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Divided 204.682 202.784 1.00936
1997 j domain protein c21orf55. [swissprot;acc:q9nx36] Subtracted 198.257 196.319 1.938
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 204.651 202.759 1.00933
1998 creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Subtracted 198.19 196.252 1.938
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Divided 200.219 198.37 1.00932
1999 acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954] Subtracted 215.799 213.865 1.934
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Divided 204.636 202.748 1.00931
2000 40s ribosomal protein s28. [swissprot;acc:p25112] Subtracted 200.343 198.427 1.916
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Divided 204.626 202.739 1.00931
2001 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Subtracted 198.258 196.346 1.912
lin-7 homolog b; lin-7b protein; likely ortholog of mouse lin-7b; mammalian lin-7 protein 2; likely orholog of mouse lin 7 homolog b (c. elegans). [refseq;acc:nm_022165] Divided 225.02 222.948 1.00929
2002 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Subtracted 208.315 206.41 1.905
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 214.775 216.769 1.00928
2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 208.315 206.41 1.00923
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Subtracted 218.466 216.562 1.904
2004 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 229.102 231.001 1.899
receptor protein-tyrosine kinase erbb-4 precursor (ec 2.7.1.112) (p180erbb4) (tyrosine kinase-type cell surface receptor her4). [swissprot;acc:q15303] Divided 225.019 222.969 1.00919
2005 epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] 222.971
sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] Subtracted 204.682 202.784 1.898
2006 lamin b1. [swissprot;acc:p20700] 218.919 220.813 1.894
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Divided 225.019 222.971 1.00919
2007 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 222.969
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Subtracted 218.919 220.812 1.893
2008 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
receptor protein-tyrosine kinase erbb-3 precursor (ec 2.7.1.112) (c-erbb3) (tyrosine kinase-type cell surface receptor her3). [swissprot;acc:p21860] Divided 225.019 222.969 1.00919
2009 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Subtracted 218.919 220.812 1.893
proteasome subunit beta type 10 precursor (ec 3.4.25.1) (proteasome mecl-1) (macropain subunit mecl-1) (multicatalytic endopeptidase complex subunit mecl-1). [swissprot;acc:p40306] Divided 216.201 214.245 1.00913
2010 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Subtracted 204.651 202.759 1.892
tubulin-specific chaperone c (tubulin-folding cofactor c) (cfc). [swissprot;acc:q15814] Divided 193.517 191.766 1.00913
2011 lamin a/c (70 kda lamin). [swissprot;acc:p02545] Subtracted 218.92 220.811 1.891
putative acyl-coa thioester hydrolase cgi-16 (ec 3.1.2.-). [swissprot;acc:q9y305] Divided 193.517 191.766 1.00913
2012 dead-box protein. [refseq;acc:nm_018665]
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 215.553 213.663 1.89
2013 protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Divided 217.662 215.693 1.00913
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 215.553 213.663 1.89

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/