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.


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 3232 to 3281 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1616 n-acetylglutamate synthase. [refseq;acc:nm_153006] High confidence 223.179 226.611 1.01538
1617 ras-related protein rap-2a. [swissprot;acc:p10114] Low confidence 202.026 197.9 1.02085
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] High confidence 221.045 217.699 1.01537
1618 rap2c, member of ras oncogene family. [refseq;acc:nm_021183] Low confidence 202.026 197.9 1.02085
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] High confidence 227.768 231.246 1.01527
1619 ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] Low confidence 200.714 196.617 1.02084
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] High confidence 227.768 231.246 1.01527
1620 adam-ts related protein 1 isoform 1; adam-ts related protein 1; thrombospondin; punctin. [refseq;acc:nm_139238] Low confidence 203.893 199.732 1.02083
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] High confidence 228.611 225.185 1.01521
1621 follicular variant translocation protein 1 precursor (fvt-1). [swissprot;acc:q06136] Low confidence 199.312 195.248 1.02081
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] High confidence 228.611 225.185 1.01521
1622 helicase ski2w (helicase-like protein) (hlp). [swissprot;acc:q15477] Low confidence 206.949 202.732 1.0208
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] High confidence 228.611 225.185 1.01521
1623 adam-tsl3 precursor (fragment). [sptrembl;acc:p82987] Low confidence 203.903 199.748 1.0208
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] High confidence 228.611 225.185 1.01521
1624 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Low confidence 201.291 197.189 1.0208
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] High confidence 230.643 227.194 1.01518
1625 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 217.446 214.2 1.01515
protein bap28. [swissprot;acc:q9h583] Low confidence 202.298 198.176 1.0208
1626 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] 205.372 201.187
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] High confidence 217.446 214.2 1.01515
1627 epsin 3. [refseq;acc:nm_017957] Low confidence 190.847 186.958 1.0208
pp1201 protein. [refseq;acc:nm_022152] High confidence 217.446 214.2 1.01515
1628 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Low confidence 205.76 201.569 1.02079
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] High confidence 217.446 214.2 1.01515
1629 dnaj homolog subfamily a member 1 (heat shock 40 kda protein 4) (dnaj protein homolog 2) (hsj-2) (hsdj). [swissprot;acc:p31689] Low confidence 197.458 193.436 1.02079
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] High confidence 217.446 214.2 1.01515
1630 40s ribosomal protein s17. [swissprot;acc:p08708] Low confidence 204.428 200.265 1.02079
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] High confidence 217.446 214.2 1.01515
1631 carnitine o-palmitoyltransferase i, mitochondrial muscle isoform (ec 2.3.1.21) (cpt i) (cpti-m) (carnitine palmitoyltransferase i like protein). [swissprot;acc:q92523] Low confidence 199.793 195.725 1.02078
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] High confidence 218.789 215.533 1.01511
1632 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Low confidence 192.879 188.955 1.02077
mitotic checkpoint protein bub3. [swissprot;acc:o43684] High confidence 221.934 218.658 1.01498
1633 zinc binding alcohol dehydrogenase, domain containing 1. [refseq;acc:nm_152444] Low confidence 197.514 193.498 1.02075
zinc finger protein 207. [swissprot;acc:o43670] High confidence 221.934 218.658 1.01498
1634 glycylpeptide n-tetradecanoyltransferase 1 (ec 2.3.1.97) (peptide n- myristoyltransferase 1) (myristoyl-coa:protein n-myristoyltransferase 1) (nmt 1) (type i n-myristoyltransferase). [swissprot;acc:p30419] Low confidence 200.654 196.575 1.02075
malonyl-coa decarboxylase, mitochondrial precursor (ec 4.1.1.9) (mcd). [swissprot;acc:o95822] High confidence 215.772 212.596 1.01494
1635 itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483]
peroxiredoxin 5, mitochondrial precursor (prx-v) (peroxisomal antioxidant enzyme) (plp) (thioredoxin peroxidase pmp20) (antioxidant enzyme b166) (aoeb166) (tpx type vi) (liver tissue 2d-page spot 71b) (alu co-repressor 1) (sbbi10). [swissprot;acc:p30044] Low confidence 201.901 197.797 1.02075
1636 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] High confidence 202.358 199.408 1.01479
gtp-binding protein rad (ras associated with diabetes) (rad1). [swissprot;acc:p55042] Low confidence 202.784 198.663 1.02074
1637 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] High confidence 202.358 199.408 1.01479
gtp-binding protein gem (gtp-binding mitogen-induced t-cell protein) (ras-like protein kir). [swissprot;acc:p55040] Low confidence 202.784 198.663 1.02074
1638 alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] 203.742 199.603
serine hydroxymethyltransferase, mitochondrial precursor (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34897] High confidence 220.686 217.481 1.01474
1639 ras (rad and gem)-like gtp-binding; gtpase ges; rem protein. [refseq;acc:nm_014012] Low confidence 202.784 198.663 1.02074
yl-1 protein (transcription factor-like 1). [swissprot;acc:q15906] High confidence 194.516 197.364 1.01464
1640 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] Low confidence 202.787 198.666 1.02074
hydroxyacylglutathione hydrolase (ec 3.1.2.6) (glyoxalase ii) (glx ii). [swissprot;acc:q16775] High confidence 194.516 197.364 1.01464
1641 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Low confidence 202.78 198.661 1.02073

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/