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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4658 to 4707 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2329 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Subtracted 5123.89 5350.78 226.89
2330 40s ribosomal protein s3a. [swissprot;acc:p49241] 4918.64 5145.39 226.75
cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] Divided 6773.67 7075.51 1.04456
2331 geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] Subtracted 5265.95 5492.28 226.33
mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198] Divided 6773.67 7075.51 1.04456
2332 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727] Subtracted 5265.95 5492.28 226.33
mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717] Divided 6773.67 7075.51 1.04456
2333 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485] Subtracted 5265.95 5492.28 226.33
thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757] Divided 6773.67 7075.51 1.04456
2334 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265] Subtracted 5265.95 5492.28 226.33
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] Divided 5123.89 5350.78 1.04428
2335 fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402] Subtracted 5265.95 5492.28 226.33
microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] Divided 5123.89 5350.78 1.04428
2336 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Subtracted 5254.55 5480.56 226.01
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] Divided 5123.89 5350.78 1.04428
2337 40s ribosomal protein s29. [swissprot;acc:p30054] Subtracted 3582.57 3357.6 224.97
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] Divided 5123.89 5350.78 1.04428
2338 60s ribosomal protein l32. [swissprot;acc:p02433] Subtracted 3618.02 3394.29 223.73
bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] Divided 5123.89 5350.78 1.04428
2339 homeobox protein otx2. [swissprot;acc:p32243] Subtracted 5682 5905.08 223.08
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] Divided 5123.89 5350.78 1.04428
2340 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 5607.81 5855.72 1.04421
homeobox protein otx1. [swissprot;acc:p32242] Subtracted 5691.1 5913.92 222.82
2341 cone-rod homeobox protein. [swissprot;acc:o43186] 5694.04 5916.78 222.74
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] Divided 5606.66 5854.45 1.0442
2342 acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19] 7007.72 7317.15 1.04416
conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Subtracted 6931.15 7152.73 221.58
2343 40s ribosomal protein s5. [swissprot;acc:p46782] Divided 3672.17 3516.98 1.04413
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Subtracted 6737.15 6957.34 220.19
2344 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]
carboxypeptidase a5. [refseq;acc:nm_080385] Divided 8353.97 8001.45 1.04406
2345 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
trifunctional purine biosynthetic protein adenosine-3 [includes: phosphoribosylamine--glycine ligase (ec 6.3.4.13) (gars) (glycinamide ribonucleotide synthetase) (phosphoribosylglycinamide synthetase); phosphoribosylformylglycinamidine cyclo-ligase (ec 6.3.3.1) (airs) (phosphoribosyl-aminoimidazole synthetase) (air synthase); phosphoribosylglycinamide formyltransferase (ec 2.1.2.2) (gart) (gar transformylase) (5'-phosphoribosylglycinamide transformylase)]. [swissprot;acc:p22102] Subtracted 5502.5 5721.43 218.93
2346 myo-inositol 1-phosphate synthase a1. [refseq;acc:nm_016368] 8695.15 8912.98 217.83
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Divided 8353.97 8001.45 1.04406
2347 arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681] Subtracted 8695.15 8912.98 217.83
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Divided 6480.27 6765.81 1.04406
2348 ral-a exchange factor ralgps2. [refseq;acc:nm_152663]
ubiquitin-like protein gdx (ubiquitin-like protein 4). [swissprot;acc:p11441] Subtracted 8695.15 8912.98 217.83
2349 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Divided 8353.97 8001.45 1.04406
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Subtracted 8695.15 8912.98 217.83
2350 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 6477.82 6695.58 217.76
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Divided 6480.27 6765.81 1.04406
2351 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Subtracted 6478.14 6695.67 217.53
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Divided 8353.97 8001.45 1.04406
2352 60s ribosomal protein l11. [swissprot;acc:p39026] Subtracted 3593.24 3375.93 217.31
coatomer epsilon subunit (epsilon-coat protein) (epsilon-cop). [swissprot;acc:o14579] Divided 8493.7 8135.59 1.04402
2353 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted 3591.95 3375.34 216.61
signal transducer and activator of transcription 5b. [swissprot;acc:p51692] Divided 5516.82 5758.48 1.0438
2354 fad synthetase. [refseq;acc:nm_025207] Subtracted 3591.95 3375.34 216.61

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/