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 green red network_comparison
Results: HTML CSV LaTeX Showing element 3958 to 4007 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
1979 tumor differentially expressed protein 1 (transmembrane protein sbbi99). [swissprot;acc:q13530] Divided 207.529 209.539 1.00969
1980 solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Subtracted 193.385 191.406 1.979
tumor differentially expressed 1 protein like. [swissprot;acc:q9nrx5] Divided 207.529 209.539 1.00969
1981 d-3-phosphoglycerate dehydrogenase (ec 1.1.1.95) (3-pgdh). [swissprot;acc:o43175]
disrupter of silencing 10. [refseq;acc:nm_020368] Subtracted 193.39 191.411 1.979
1982 40s ribosomal protein s28. [swissprot;acc:p25112] Divided 198.427 200.343 1.00966
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Subtracted 193.389 191.41 1.979
1983 lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Divided 217.175 219.25 1.00955
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Subtracted 193.387 191.408 1.979
1984 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Divided 217.193 219.26 1.00952
similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4] Subtracted 193.394 191.415 1.979
1985 lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] 223.041 225.015 1.974
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Divided 217.193 219.26 1.00952
1986 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Subtracted 198.935 196.964 1.971
1987 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Divided 222.9 225.022 1.00952
1988 9 kda protein. [swissprot;acc:p13994] 217.193 219.26
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 198.936 196.965 1.971
1989 collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Divided 217.195 219.261 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 215.693 217.662 1.969
1990 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided 217.194 219.26 1.00951
protein phosphatase 1, regulatory (inhibitor) subunit 12a; myosin phosphatase, target subunit 1. [refseq;acc:nm_002480] Subtracted 215.709 217.676 1.967
1991 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 215.979 217.941 1.962
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Divided 217.194 219.26 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 214.245 216.201 1.956
zasp protein (fragment). [sptrembl;acc:q9y4z3] Divided 217.207 219.267 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 196.347 198.3 1.953
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Divided 190.835 189.052 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 196.341 198.293 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 190.787 189.011 1.0094
1995 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] 190.73 188.961 1.00936
peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347] Subtracted 196.319 198.258 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 202.784 204.682 1.00936
1997 j domain protein c21orf55. [swissprot;acc:q9nx36] Subtracted 196.319 198.257 1.938
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Divided 202.759 204.651 1.00933
1998 creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277] Subtracted 196.252 198.19 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 198.37 200.219 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 213.865 215.799 1.934
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Divided 202.748 204.636 1.00931
2000 40s ribosomal protein s28. [swissprot;acc:p25112] Subtracted 198.427 200.343 1.916
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Divided 202.739 204.626 1.00931
2001 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Subtracted 196.346 198.258 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 222.948 225.02 1.00929
2002 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Subtracted 206.41 208.315 1.905
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 216.769 214.775 1.00928
2003 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] 206.41 208.315 1.00923
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Subtracted 216.562 218.466 1.904
2004 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] 231.001 229.102 1.899

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/