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 Network Comparison Type red Value Type Rank green Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1558 to 1607 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
Rank
green
description
network_comparison
5603.24 2710 5583.64 similar to nuclear protein e3-3 orf1. [sptrembl;acc:q9bu61] 1.00351
2712 a kindred of iglon. [refseq;acc:nm_173808]
2713 ankyrin-repeat family a protein 2 (rfxank-like 2). [swissprot;acc:q9h9e1]
2714 inflammation-related g protein-coupled receptor ex33. [refseq;acc:nm_020370]
2717 palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]
2718 beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]
2719 syntaxin 16 (syn16). [swissprot;acc:o14662]
2720 27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
2721 syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]
2722 alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
2723 adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]
2724 synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]
2725 syntaxin 1b. [swissprot;acc:q15531]
2727 melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]
2728 dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
5606.66 2341 5854.45 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] 1.0442
5607.43 846 6194.98 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] 1.10478
5607.81 2340 5855.72 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 1.04421
5608.22 2576 5712.39 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] 1.01857
5608.38 2575 5712.59 rho interacting protein 3. [refseq;acc:nm_015134] 1.01858
5613.16 1403 6050.16 importin 4. [refseq;acc:nm_024658] 1.07785
5620.55 2118 5926.71 guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] 1.05447
5622.89 757 6260.02 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] 1.11331
5623.18 834 6218.77 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] 1.10592
835 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2]
5628.21 936 6180.37 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] 1.09811
5628.53 1421 6063.61 importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 1.0773
1422 importin 8; ran-binding protein 8. [refseq;acc:nm_006390]
1423 brefeldin a-inhibited guanine nucleotide-exchange protein 2 (brefeldin a-inhibited gep 2). [swissprot;acc:q9y6d5]
1424 hsgcn1 (fragment). [sptrembl;acc:q99736]
1425 brefeldin a-inhibited guanine nucleotide-exchange protein 1 (brefeldin a-inhibited gep 1) (p200 arf-gep1) (p200 arf guanine nucleotide exchange factor). [swissprot;acc:q9y6d6]
5633.44 1816 5997 potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] 1.06454
1817 solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7]
1818 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]
1819 adp-ribosylation factor 4. [swissprot;acc:p18085]
1820 fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476]
1821 shc transforming protein. [swissprot;acc:p29353]
1822 zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389]
1823 neuronal shc. [refseq;acc:nm_016848]
1824 adp-ribosylation factor 1. [swissprot;acc:p32889]
1825 heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]
1826 adp-ribosylation factor 3. [swissprot;acc:p16587]
1827 protein sck (fragment). [swissprot;acc:p98077]
1828 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]
1829 ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830]
1830 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
1831 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]
1832 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]
5633.67 1515 6050.69 lanc lantibiotic synthetase component c-like 2; testis-specific adriamycin sensitivity protein; lanc (bacterial lantibiotic synthetase component c)-like 2; g protein-coupled receptor 69b. [refseq;acc:nm_018697] 1.07402
1516 lanthionine synthetase c-like protein 1; g protein-coupled receptor 69a; lanc (bacterial lantibiotic synthetase component c)-like 1; lanc (bacterial lantibiotic synthetase component). [refseq;acc:nm_006055]

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/