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 4008 to 4057 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1002 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Ranked 225.167 217.922 1.03325
1003 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Squared 17541.4 20148.6 1.14863
ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Rooted 59.2915 62.5118 1.05431
seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Measured 5680.76 6220.45 1.095
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Ranked 225.167 217.922 1.03325
1004 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Squared 17541.4 20148.6 1.14863
interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Rooted 61.5654 64.9046 1.05424
o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Measured 5391.64 5903.72 1.09498
sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Ranked 238.725 231.059 1.03318
1005 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] Measured 5780.34 6329.3 1.09497
dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Ranked 225.448 218.232 1.03307
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Squared 17541.4 20148.6 1.14863
xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Rooted 64.9107 68.4287 1.0542
1006 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Ranked 116.524 120.375 1.03305
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Squared 17541.4 20148.6 1.14863
kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Rooted 59.3039 62.5177 1.05419
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Measured 5707.73 6249.1 1.09485
1007 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Squared 17603.1 20218.5 1.14858
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Measured 5707.73 6249.1 1.09485
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Rooted 64.0132 67.4724 1.05404
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Ranked 162.055 156.884 1.03296
1008 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Squared 17603.1 20218.5 1.14858
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Rooted 51.2693 54.0336 1.05392
single-minded homolog 1. [swissprot;acc:p81133] Measured 5707.73 6249.1 1.09485
wd-repeat protein bing4. [swissprot;acc:o15213] Ranked 243.227 235.475 1.03292
1009 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Squared 21492.5 24677.4 1.14819
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Ranked 229.116 221.823 1.03288
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Rooted 58.8768 62.0483 1.05387
synapsin iii. [swissprot;acc:o14994] Measured 5791.82 6340.86 1.0948
1010 aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Rooted 62.0618 65.4025 1.05383
peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Ranked 217.523 210.648 1.03264
proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Squared 24025.9 27585.7 1.14817
1011 elks protein. [refseq;acc:nm_015064] Rooted 62.0618 65.4025 1.05383
hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Measured 5791.82 6340.86 1.0948
molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Squared 24025.9 27585.7 1.14817
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Ranked 217.026 210.189 1.03253
1012 actin binding lim protein 2. [refseq;acc:nm_032432] Measured 5791.82 6340.86 1.0948
anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Squared 24025.9 27585.7 1.14817
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Rooted 74.9231 78.9471 1.05371
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Ranked 217.021 210.185 1.03252
1013 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Squared 24025.9 27585.7 1.14817
hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Measured 5791.82 6340.86 1.0948
heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Rooted 58.0289 61.136 1.05354
protein bap28. [swissprot;acc:q9h583] Ranked 244.312 236.647 1.03239
1014 apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 235.422 1.03238
n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Rooted 58.0289 61.136 1.05354
proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Squared 24025.9 27585.7 1.14817
synapsin ii. [swissprot;acc:q92777] Measured 5791.82 6340.86 1.0948
1015 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Ranked 221.73 228.906 1.03236

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/