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 3180 to 3229 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1590 ras-related protein rab-5b. [swissprot;acc:p35239] Low confidence 7969.92 8238.53 1.0337
1591 multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] High confidence 6364.01 6819.38 1.07155
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Low confidence 7782.52 8044.76 1.0337
1592 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] High confidence 5853.1 6271.79 1.07153
serine/threonine kinase 38 like. [refseq;acc:nm_015000] Low confidence 8152.52 8427.18 1.03369
1593 proliferating cell nuclear antigen (pcna) (cyclin). [swissprot;acc:p12004] High confidence 4977.77 5333.78 1.07152
stress-70 protein, mitochondrial precursor (75 kda glucose regulated protein) (grp 75) (peptide-binding protein 74) (pbp74) (mortalin) (mot). [swissprot;acc:p38646] Low confidence 8068.55 8340.4 1.03369
1594 atp-dependent dna helicase q1 (dna-dependent atpase q1). [swissprot;acc:p46063] 8147.51 8421.91 1.03368
transportin-sr; importin 12. [refseq;acc:nm_012470] High confidence 5184.94 5555.76 1.07152
1595 cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493] Low confidence 8549.01 8270.52 1.03367
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] High confidence 6351.32 6805.39 1.07149
1596 enigma protein; lim domain protein. [refseq;acc:nm_005451] 5665.34 6070.32 1.07148
spermatogenesis associated factor spaf. [refseq;acc:nm_145207] Low confidence 7913.23 8179.69 1.03367
1597 eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371] High confidence 5665.34 6070.32 1.07148
ras-related protein rab-5c (rab5l) (l1880). [swissprot;acc:p51148] Low confidence 7969.65 8238.02 1.03367
1598 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] High confidence 5068.17 5430.41 1.07147
sterile alpha and tir motif containing 1; sterile alpha and heat/armadillo motif protein, ortholog of drosophila. [refseq;acc:nm_015077] Low confidence 7961.17 8229.2 1.03367
1599 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] High confidence 5184.45 5554.97 1.07147
dok-like protein. [refseq;acc:nm_024872] Low confidence 7889.23 8154.7 1.03365
1600 14.5 kda translational inhibitor protein (p14.5) (uk114 antigen homolog). [swissprot;acc:p52758] High confidence 6336.22 6788.96 1.07145
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Low confidence 7889.23 8154.7 1.03365
1601 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]
spectrin beta chain, brain 2 (spectrin, non-erythroid beta chain 2) (beta-iii spectrin). [swissprot;acc:o15020] High confidence 5232.14 5605.8 1.07142
1602 mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Low confidence 8049.75 8320.53 1.03364
spectrin beta chain, brain 1 (spectrin, non-erythroid beta chain 1) (beta-ii spectrin) (fodrin beta chain). [swissprot;acc:q01082] High confidence 5232.14 5605.8 1.07142
1603 membrane associated progesterone receptor component 1 (mpr). [swissprot;acc:o00264] Low confidence 8000.22 8269.25 1.03363
phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394] High confidence 5232.14 5605.8 1.07142
1604 malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] 6176.82 6617.91 1.07141
proprotein convertase subtilisin/kexin type 9 preproprotein; neural apoptosis regulated convertase 1; hypercholesterolemia, autosomal dominant 3. [refseq;acc:nm_174936] Low confidence 7973.26 8241.35 1.03362
1605 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] High confidence 6176.82 6617.91 1.07141
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] Low confidence 7880.71 8145.66 1.03362
1606 5'-methylthioadenosine phosphorylase (ec 2.4.2.28) (mta phosphorylase) (mtapase). [swissprot;acc:q13126] High confidence 5232.99 5606.53 1.07138
heat shock factor protein 2 (hsf 2) (heat shock transcription factor 2) (hstf 2). [swissprot;acc:q03933] Low confidence 8141.09 8414.68 1.03361
1607 putative ribosomal rna methyltransferase 1 (ec 2.1.1.-) (rrna (uridine-2'-o-)-methyltransferase) (jm23 protein). [swissprot;acc:q9uet6] High confidence 5232.99 5606.53 1.07138
syntaxin 18. [swissprot;acc:q9p2w9] Low confidence 7839.44 8102.81 1.0336
1608 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
ubiquitin. [swissprot;acc:p02248] High confidence 6158.22 6597.55 1.07134
1609 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 5826.74 6242.44
heat shock factor protein 4 (hsf 4) (heat shock transcription factor 4) (hstf 4) (hhsf4). [swissprot;acc:q9ulv5] Low confidence 8141.75 8415.33 1.0336
1610 eif-5a2 protein. [refseq;acc:nm_020390] High confidence 6222.4 6665.83 1.07126
ikappab kinase complex-associated protein (ikk complex-associated protein) (p150). [swissprot;acc:o95163] Low confidence 7843.41 8106.95 1.0336
1611 cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] High confidence 5497.73 5132.35 1.07119
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Low confidence 7703.86 7962.64 1.03359
1612 eukaryotic translation initiation factor 5a (eif-5a) (eif-4d) (rev- binding factor). [swissprot;acc:p10159] High confidence 6212.98 6655.12 1.07116
zinc finger protein 277. [swissprot;acc:q9nrm2] Low confidence 7691.32 7949.57 1.03358
1613 igf-ii mrna-binding protein 1. [refseq;acc:nm_006546] 7815.17 8077.42 1.03356
mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] High confidence 6035.6 6464.5 1.07106
1614 nefa-interacting nuclear protein nip30. [refseq;acc:nm_024946]
ras-related protein rab-5a. [swissprot;acc:p20339] Low confidence 7968.53 8235.92 1.03356
1615 lim homeobox transcription factor 1 alpha (lim/homeobox protein lmx1a) (lim-homeobox protein 1.1) (lmx-1.1). [swissprot;acc:q8te12] High confidence 6035.6 6464.5 1.07106

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/