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 1980 to 2029 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
248 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Measured 0 1225.09 1079.37 1.135
myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7] Squared 1 8875.01 6768.05 1.31131
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Measured 6417.18 7859.6 1.22477
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Rooted 56.0466 63.4808 1.13264
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Squared 0 42556.5 33335.4 1.27662
249 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 35446.2 27772 1.27633
glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217] 1 8875.01 6768.05 1.31131
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Rooted 0 23.5797 26.096 1.10671
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] Measured 1225.08 1079.37 1.135
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Ranked 10551.6 11573.7 1.09687
ns1-associated protein 1. [refseq;acc:nm_006372] 1 237.302 212.41 1.11719
transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] Rooted 55.5965 62.9349 1.13199
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Measured 6417.18 7859.59 1.22477
250 c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545] Squared 69201.8 53013.4 1.30536
dc11 protein. [refseq;acc:nm_020186] Rooted 0 23.5797 26.096 1.10671
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Squared 504.762 643.571 1.275
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Ranked 1 237.302 212.41 1.11719
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] 0 10551.6 11573.7 1.09687
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Measured 1225.08 1079.37 1.135
nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] Rooted 1 55.5965 62.9349 1.13199
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Measured 6417.18 7859.6 1.22477
251 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted 0 21.3142 23.5833 1.10646
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844] Squared 1 69165.6 52992.1 1.30521
keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] Ranked 0 10551.6 11573.6 1.09686
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Measured 1225.08 1079.38 1.13498
max protein. [swissprot;acc:p25912] Rooted 1 56.3054 63.7148 1.13159
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Ranked 186.172 166.661 1.11707
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Measured 6417.18 7859.6 1.22477
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Squared 0 25574.2 20063.8 1.27464
252 crk-like protein. [swissprot;acc:p46109] Measured 1 6417.18 7859.6 1.22477
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Ranked 237.292 212.457 1.11689
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] 0 10551.6 11573.5 1.09685
lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] Rooted 21.1331 19.1063 1.10608
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 1 51.6736 58.4422 1.13099
pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148] Squared 69165 52991.7 1.3052
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 0 803.941 631.169 1.27373
star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095] Measured 1225.08 1079.38 1.13498
253 b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182] Squared 1 69165 52991.7 1.3052
espin. [refseq;acc:nm_031475] Measured 0 1225.07 1079.38 1.13498
keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] Ranked 10551.6 11573.5 1.09685
mad protein (max dimerizer). [swissprot;acc:q05195] 1 228 204.333 1.11583
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared 0 46977 36903.3 1.27298
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Measured 1 6417.18 7859.59 1.22477
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Rooted 0 8.05424 8.90701 1.10588
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1 53.5956 60.465 1.12817
254 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Measured 0 1318.22 1495.66 1.13461
adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] Squared 220.878 173.801 1.27087
keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854] Ranked 10551.6 11573.5 1.09685
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Measured 1 6417.18 7859.6 1.22477
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Rooted 0 8.05424 8.90701 1.10588

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/