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 3780 to 3829 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1890 zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Subtracted 5633.44 5997 363.56
1891 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Divided 5438.18 5782.62 1.06334
neuronal shc. [refseq;acc:nm_016848] Subtracted 5633.44 5997 363.56
1892 adp-ribosylation factor 1. [swissprot;acc:p32889]
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] Divided 5438.52 5783.01 1.06334
1893 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 6830.4 7261.98 1.06319
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Subtracted 5633.44 5997 363.56
1894 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 3598.08 3384.59 1.06308
adp-ribosylation factor 3. [swissprot;acc:p16587] Subtracted 5633.44 5997 363.56
1895 protein sck (fragment). [swissprot;acc:p98077]
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Divided 5882.1 6252.66 1.063
1896 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Subtracted 5633.44 5997 363.56
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Divided 4521 4805.16 1.06285
1897 ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] Subtracted 5633.44 5997 363.56
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Divided 4590.74 4879.11 1.06282
1898 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 6885.11 7317.48 1.0628
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 5633.44 5997 363.56
1899 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Divided 5786.36 6149.1 1.06269
solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] Subtracted 5633.44 5997 363.56
1900 dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]
seven in absentia homolog 2. [refseq;acc:nm_005067] Divided 5399.47 5737.79 1.06266
1901 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 5204.25 5530.11 1.06261
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Subtracted 5786.36 6149.1 362.74
1902 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 6884.69 7247.36 362.67
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Divided 5204.25 5530.11 1.06261
1903 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Subtracted 6952.66 7315.06 362.4
1904 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Divided 5204.25 5530.11 1.06261
kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679] Subtracted 6952.66 7315.06 362.4
1905 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Divided 7497.96 7967.09 1.06257
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Subtracted 6952.66 7315.06 362.4
1906 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 5068.17 5430.41 362.24
mitochondrial ribosomal protein l18. [refseq;acc:nm_014161] Divided 5396.61 5733.93 1.06251
1907 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Subtracted 5384.89 5746.51 361.62
hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] Divided 6858.84 7287.27 1.06246
1908 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] Subtracted 6437.24 6797.24 360
dc11 protein. [refseq;acc:nm_020186] Divided 6858.84 7287.27 1.06246
1909 amyloid beta precursor protein-binding protein 1; amyloid protein-binding protein 1. [refseq;acc:nm_003905]
enhancer of rudimentary homolog. [swissprot;acc:q14259] Subtracted 6437.24 6797.24 360
1910 5-aminolevulinic acid synthase, erythroid-specific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-e). [swissprot;acc:p22557] Divided 6858.84 7287.27 1.06246
translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [swissprot;acc:p49770] Subtracted 5456.57 5816.14 359.57
1911 brain protein 16. [refseq;acc:nm_016458] 5774.02 6133.01 358.99
ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968] Divided 6858.84 7287.27 1.06246
1912 dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6] Subtracted 5386.37 5744.89 358.52
ubiquitin-activating enzyme e1 (a1s9 protein). [swissprot;acc:p22314] Divided 6858.84 7287.27 1.06246
1913 calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]
zinc finger protein 258. [refseq;acc:nm_145310] Subtracted 5386.37 5744.89 358.52
1914 melanoma antigen recognized by t cells 2. [refseq;acc:nm_018194] Divided 6858.84 7287.27 1.06246
zinc finger protein 261 (dxs6673e protein). [swissprot;acc:q14202] Subtracted 5386.37 5744.89 358.52
1915 5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196] Divided 6858.84 7287.27 1.06246

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/