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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Gene Rank description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 951 to 1000 of 9634 in total
Network Comparison Type  : Divided
Value Type  : Measured
Rank
description
Interaction Map
Filtered
red
network_comparison
green
238 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] High confidence 1 27642.5 1.23182 22440.4
zinc finger protein 415. [refseq;acc:nm_018355] Low confidence 0 2352.12 1.19448 1969.15
239 carboxypeptidase b precursor. [refseq;acc:nm_020361] High confidence 1 7711.38 1.23071 6265.8
dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] Low confidence 6456.05 1.06449 6872.38
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] High confidence 0 382.142 1.13666 434.366
zinc finger protein 35 (zinc finger protein hf.10). [swissprot;acc:p13682] Low confidence 2352.27 1.19448 1969.29
240 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] High confidence 1 7711.36 1.23071 6265.79
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 0 1475.83 1.13575 1676.18
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 1 7671.08 1.06425 8163.95
zinc finger protein 10 (zinc finger protein kox1) (fragment). [swissprot;acc:p21506] 0 2352.16 1.19448 1969.19
241 glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335] 1 4585.58 1.06356 4311.52
keratin associated protein 9.2. [refseq;acc:nm_031961] High confidence 0 1225.47 1.13574 1079.01
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 1 7711.31 1.23071 6265.76
zinc finger protein 225. [swissprot;acc:q9uk10] Low confidence 0 2352.16 1.19448 1969.19
242 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926] 1 4585.58 1.06356 4311.52
max protein. [swissprot;acc:p25912] High confidence 4640.26 1.22943 5704.87
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 0 729.216 1.13524 642.343
zinc finger protein 256 (bone marrow zinc finger 3) (bmzf-3). [swissprot;acc:q9y2p7] Low confidence 2352.16 1.19448 1969.19
243 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] 1 7648.9 1.06338 8133.69
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] High confidence 4246.95 1.22652 5208.98
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] 0 1225.09 1.13502 1079.36
zinc finger protein 214 (bwscr2 associated zinc-finger protein 1) (baz 1). [swissprot;acc:q9ul59] Low confidence 2352.16 1.19448 1969.19
244 dj54b20.2 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q96qh9] 2352.23 1969.25
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] High confidence 1225.09 1.13502 1079.36
protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481] Low confidence 1 8759.92 1.06331 9314.48
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] High confidence 4250.14 1.22614 5211.25
245 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4251.65 1.22595 5212.33
keratin associated protein 1.5. [refseq;acc:nm_031957] 0 1225.09 1.13502 1079.36
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Low confidence 1 8509.99 1.06313 9047.26
zinc finger protein 165 (ld65). [swissprot;acc:p49910] 0 2352.16 1.19448 1969.19
246 ba526d8.4 (novel krab box containing c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9h559] 2352.23 1969.25
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] High confidence 1 4252.66 1.22583 5213.05
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] 0 1225.09 1.13502 1079.36
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Low confidence 1 8509.76 1.06312 9046.87
247 cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] 8509.51 1.0631 9046.45
dj153g14.3 (novel c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9ujn7] 0 2352.07 1.19448 1969.11
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] High confidence 1225.09 1.13502 1079.36
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] 1 6416.68 1.22574 7865.15
248 keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060] 0 1225.09 1.135 1079.37
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] 1 6417.18 1.22477 7859.6
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Low confidence 7615.71 1.06302 8095.68
zinc finger protein 264. [swissprot;acc:o43296] 0 2352.12 1.19448 1969.15
249 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 10547.4 1.06276 9924.56
keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059] High confidence 0 1225.08 1.135 1079.37
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] 1 6417.18 1.22477 7859.59
zinc finger protein 228. [swissprot;acc:q9uju3] Low confidence 0 2352.23 1.19448 1969.25
250 keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8] High confidence 1225.08 1.135 1079.37
large neutral amino acids transporter small subunit 2 (l-type amino acid transporter 2) (hlat2). [swissprot;acc:q9uhi5] Low confidence 1 6975.98 1.06261 7412.76
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] High confidence 6417.18 1.22477 7859.6
zinc finger protein 224. [swissprot;acc:q9nzl3] Low confidence 0 2352.49 1.19447 1969.49

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/