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 6008 to 6057 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
751 u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Ranked Divided 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
cerebral cell adhesion molecule. [refseq;acc:nm_016174] Measured Subtracted 9596.59 10241.9 645.31
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Squared 41510.6 37375.2 4135.4
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Rooted 51.5667 55.8498 4.2831
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Ranked 210.946 221.225 10.279
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 Divided 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
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Measured Subtracted 6194.15 6839.37 645.22
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Ranked 210.946 221.225 10.279
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 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
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Rooted Subtracted 60.8463 65.123 4.2767
solute carrier family 27 (fatty acid transporter), member 4; fatty acid transport protein 4. [refseq;acc:nm_005094] Squared 27404 31534 4130
754 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Rooted Divided 66.9737 71.4637 1.06704
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 51.5881 47.3127 4.2754
branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687] Squared Divided 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
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Subtracted 6194.15 6839.37 645.22
solute carrier family 27 member 3; fatty acid transport protein 3. [refseq;acc:nm_024330] Squared 27403.7 31533.7 4130
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Ranked 210.946 221.225 10.279
755 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 224.244 234.511 10.267
5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Rooted Divided 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
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Rooted Subtracted 60.7498 65.0218 4.272
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Measured 4651.88 5296.78 644.9
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 Divided 224.434 235.583 1.04968
very long-chain acyl-coa synthetase homolog 1. [refseq;acc:nm_014031] Squared Subtracted 27403.4 31533.4 4130
756 40s ribosomal protein s21. [swissprot;acc:p35265] Ranked 224.244 234.511 10.267
5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Rooted Divided 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
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Rooted Subtracted 60.7498 65.0218 4.272
solute carrier family 27 (fatty acid transporter), member 5; very long-chain acyl-coa synthetase homolog 2; very long-chain acyl-coa synthetase-related protein; likely ortholog of mouse solute carrier family 27 (fatty acid transporter), member 5. [refseq;acc:nm_012254] Squared 27403.6 31533.6 4130
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Measured 4651.88 5296.78 644.9
topoisomerase-related function protein 4-2. [refseq;acc:nm_022447] Divided 4725.28 5261.06 1.11339
transducin-like enhancer protein 4. [swissprot;acc:q04727] Squared 31298 36502 1.16627
757 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Rooted Subtracted 50.5505 46.2797 4.2708
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Ranked Divided 224.434 235.583 1.04968
cytoplasmic antiproteinase 3 (cap3) (cap-3) (protease inhibitor 9) (serpin b9). [swissprot;acc:p50453] Subtracted 224.244 234.511 10.267
delta(14)-sterol reductase (ec 1.3.1.70) (c-14 sterol reductase) (sterol c14-reductase) (delta14-sr) (transmembrane 7 superfamily member 2) (another new gene 1) (putative sterol reductase sr-1). [swissprot;acc:o76062] Squared 27403.4 31533.3 4129.9
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Measured 4651.88 5296.78 644.9
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Divided 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

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/