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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Value Type Interaction Map green Gene Filtered Rank description Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 2625 to 2674 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
green
Rank
description
network_comparison
red
228.698 919 midasin (midas-containing protein). [swissprot;acc:q9nu22] 1.03725 237.218
228.752 203 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 1.13516 201.515
204 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
228.762 901 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] 1.03872 237.62
902 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]
228.769 1590 thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] 1.01621 225.119
1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
1592 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470]
1593 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
228.784 202 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 1.13553 201.478
228.795 1366 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 1.02194 223.884
228.797 1364 serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] 223.885
228.799 1367 neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] 223.887
228.805 1360 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] 1.02195 223.89
228.906 1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] 1.03236 221.73
228.934 118 nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1.24382 284.753
229.2 1451 my016 protein. [sptrembl;acc:q9h3k6] 1.01978 224.755
229.35 694 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 1.05475 241.907
229.411 432 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] 1.07934 212.547
433 programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]
434 t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]
229.549 646 short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] 1.05914 216.731
647 dynein light chain 2. [refseq;acc:nm_080677]
229.565 520 sqv-7-like protein (fragment). [sptrembl;acc:o95454] 1.06897 214.754
229.573 1438 geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 1.02015 225.039
1439 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]
1440 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]
1441 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]
1442 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]
229.677 959 guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] 1.03431 237.558
960 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543]
229.766 1449 transportin-sr; importin 12. [refseq;acc:nm_012470] 1.0198 225.305
230.07 521 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 1.06891 215.237
523 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]
524 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]
525 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]
230.242 1154 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 1.02646 224.307
1155 inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869]
1156 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
1157 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170]
230.294 2331 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 1.00452 229.258
2332 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
2333 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
2334 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
2335 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
2336 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
2337 homeobox protein dlx-2. [swissprot;acc:q07687]
2338 homeobox protein dlx-5. [swissprot;acc:p56178]
2339 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
2340 homeobox protein dlx-3. [swissprot;acc:o60479]

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/