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 3001 to 3050 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
751 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Rooted 66.9738 71.4638 1.06704
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Squared 20305.9 23689.4 1.16663
myosin light chain 1, slow-twitch muscle b/ventricular isoform (mlc1sb) (alkali). [swissprot;acc:p08590] Measured 4565.34 5085.92 1.11403
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked 223.463 212.875 1.04974
752 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Rooted 66.9736 71.4636 1.06704
nadh-ubiquinone oxidoreductase 13 kda-a subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-a) (ci-13kd-a). [swissprot;acc:o75380] Measured 4565.34 5085.92 1.11403
step ii splicing factor slu7. [refseq;acc:nm_006425] Ranked 223.463 212.875 1.04974
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Squared 20305.9 23689.4 1.16663
753 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Rooted 66.9737 71.4637 1.06704
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] Squared 24183.6 28211.1 1.16654
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Ranked 224.434 235.583 1.04968
myosin light chain 1, slow-twitch muscle a isoform (mlc1sa) (alkali). [swissprot;acc:p14649] Measured 4565.34 5085.92 1.11403
754 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Rooted 66.9737 71.4637 1.06704
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared 23958.6 27945.1 1.16639
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Ranked 224.434 235.583 1.04968
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Measured 4565.34 5085.92 1.11403
755 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Rooted 66.9737 71.4637 1.06704
branched-chain amino acid aminotransferase, mitochondrial precursor (ec 2.6.1.42) (bcat(m)) (placental protein 18) (pp18). [swissprot;acc:o15382] Squared 23966.4 27952.2 1.16631
nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] Measured 4079.81 4545.01 1.11402
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] Ranked 224.434 235.583 1.04968
756 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Rooted 66.9737 71.4637 1.06704
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Ranked 224.434 235.583 1.04968
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Measured 4725.28 5261.06 1.11339
transducin-like enhancer protein 4. [swissprot;acc:q04727] Squared 31298 36502 1.16627
757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Ranked 224.434 235.583 1.04968
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Measured 5622.89 6260.02 1.11331
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Squared 20248.9 23608.3 1.16591
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Rooted 60.4457 64.4918 1.06694
758 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Measured 3760.3 4185.82 1.11316
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Squared 20248.9 23608.3 1.16591
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Ranked 224.434 235.583 1.04968
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] Rooted 96.6463 103.103 1.06681
759 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] Measured 4254.62 4736.03 1.11315
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Squared 49280.5 42272.7 1.16578
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Rooted 66.9416 71.4055 1.06668
osteoclast stimulating factor 1. [swissprot;acc:q92882] Ranked 231.809 243.289 1.04952
760 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Measured 5870.2 6533.39 1.11298
c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Squared 21186.4 24698.3 1.16576
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Rooted 66.9397 71.4023 1.06667
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Ranked 246.055 234.458 1.04946
761 alpha-nac protein. [sptrembl;acc:q9h009] Rooted 66.9404 71.4035 1.06667
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Ranked 213.325 203.303 1.0493
translation initiation factor if-2. [swissprot;acc:o60841] Measured 5811.51 6467.62 1.1129
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Squared 21186.4 24698.3 1.16576
762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Ranked 213.256 203.237 1.0493
di-ras2. [refseq;acc:nm_017594] Rooted 66.9397 71.4022 1.06666
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Measured 6231.31 6933.9 1.11275
pp1201 protein. [refseq;acc:nm_022152] Squared 21186.4 24698.3 1.16576
763 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] Measured 4250.54 4729.67 1.11272
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Squared 21186.4 24698.3 1.16576

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/