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 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
398 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked High confidence 218.818 238.358 1.0893
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted 116.707 106.044 1.10055
serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] Squared Low confidence 50510.9 47246.5 1.06909
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured High confidence 5084.26 5904.1 1.16125
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked Low confidence 205.997 213.496 1.0364
399 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952] Rooted 84.6421 88.7007 1.04795
atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p2) (atpase protein 9) (atpase subunit c). [swissprot;acc:q06055] Squared 52285.1 48907.2 1.06907
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked High confidence 207.889 226.226 1.08821
cyclin g2. [swissprot;acc:q16589] Rooted 116.707 106.044 1.10055
dimethylaniline monooxygenase [n-oxide forming] 4 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 4) (fmo 4) (dimethylaniline oxidase 4). [swissprot;acc:p31512] Measured Low confidence 7680.62 8085.57 1.05272
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared High confidence 18929.1 23222.8 1.22683
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured 5201.41 4479.76 1.16109
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Ranked Low confidence 193.291 186.506 1.03638
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Measured High confidence 5201.41 4479.76 1.16109
cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 116.707 106.044 1.10055
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Squared Low confidence 45694.9 42750.3 1.06888
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] High confidence 39478.8 48419 1.22646
mad protein (max dimerizer). [swissprot;acc:q05195] Measured Low confidence 6970.25 7337.73 1.05272
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked High confidence 207.908 226.218 1.08807
solute carrier family 35, member e1. [refseq;acc:nm_024881] Low confidence 203.661 211.03 1.03618
tumor protein p73-like; tumor protein 63 kda with strong homology to p53; tumor protein p63. [refseq;acc:nm_003722] Rooted 75.7411 79.3726 1.04795
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured High confidence 5201.41 4479.76 1.16109
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 40524.8 1.22638
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Measured Low confidence 10800.7 10260 1.0527
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Squared 45694.9 42750.3 1.06888
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked High confidence 207.908 226.218 1.08807
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 116.707 106.044 1.10055
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Ranked Low confidence 205.017 197.863 1.03616
tumor protein p73 (p53-like transcription factor) (p53-related protein). [swissprot;acc:o15350] Rooted 75.7395 79.3703 1.04794
402 ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] Squared 48608.6 45485.7 1.06866
cellular tumor antigen p53 (tumor suppressor p53) (phosphoprotein p53) (antigen ny-co-13). [swissprot;acc:p04637] Rooted 75.7377 79.3677 1.04793
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared High confidence 39472 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured 5201.41 4479.76 1.16109
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 207.908 226.218 1.08807
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Measured Low confidence 7934.21 8352.26 1.05269
x-linked protein sts1769. [swissprot;acc:q99871] Ranked 211.253 203.883 1.03615
403 elongation factor 1-beta (ef-1-beta). [swissprot;acc:p24534] Rooted 70.3162 73.6827 1.04788
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured High confidence 5201.41 4479.76 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 59.6834 65.6741 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
prolyl endopeptidase (ec 3.4.21.26) (post-proline cleaving enzyme) (pe). [swissprot;acc:p48147] Squared Low confidence 48608.6 45485.7 1.06866
seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81] Measured 8853.13 9319.56 1.05269
three prime repair exonuclease 1 isoform c; deoxyribonuclease iii, dnaq/mutd (e. coli)-like; 3' repair exonuclease 1; atr interacting protein. [refseq;acc:nm_032166] Ranked 211.253 203.883 1.03615
404 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared High confidence 26819.1 32855.4 1.22507
atp synthase lipid-binding protein, mitochondrial precursor (ec 3.6.3.14) (atp synthase proteolipid p3) (atpase protein 9) (atpase subunit c). [swissprot;acc:p48201] Low confidence 52108.1 48765.3 1.06855
dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Rooted 72.2476 75.7022 1.04782
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked High confidence 207.908 226.218 1.08807
kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241] Measured Low confidence 10008.8 9508.16 1.05265

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/