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 6908 to 6957 of 19268 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1055 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted High confidence 138.705 132.538 6.167
neuronal cell death inducible putative kinase (skip3). [swissprot;acc:q96ru7] Low confidence 203.522 198.791 4.731
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 199.656 194.966 1.02406
1056 g-protein-coupled receptor induced protein. [refseq;acc:nm_025195] Subtracted 203.52 198.79 4.73
methyltransferase like 2. [refseq;acc:nm_018396] High confidence 147.211 153.371 6.16
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided Low confidence 202.569 197.815 1.02403
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] High confidence 219.01 212.468 1.03079
1057 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
carnitine palmitoyltransferase i related c. [refseq;acc:nm_152359] Subtracted Low confidence 203.519 198.789 4.73
cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] High confidence 147.211 153.371 6.16
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided Low confidence 202.569 197.815 1.02403
1058 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] High confidence 228.105 221.293 1.03078
bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Low confidence 198.804 194.142 1.02401
carnitine o-palmitoyltransferase i, mitochondrial liver isoform (ec 2.3.1.21) (cpt i) (cpti-l). [swissprot;acc:p50416] Subtracted 203.519 198.789 4.73
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] High confidence 147.211 153.371 6.16
1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided 228.105 221.293 1.03078
cationic amino acid transporter-4 (cat-4) (cat4). [swissprot;acc:o43246] Low confidence 200.552 195.852 1.024
er lumen protein retaining receptor 2 (kdel receptor 2) (elp-1). [swissprot;acc:p33947] Subtracted 202.92 198.191 4.729
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] High confidence 147.211 153.371 6.16
1060 er lumen protein retaining receptor 1 (kdel receptor 1). [swissprot;acc:p24390] Low confidence 202.92 198.191 4.729
nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Divided High confidence 218.162 211.648 1.03078
septin 6. [swissprot;acc:q14141] Subtracted 126.604 120.463 6.141
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided Low confidence 203.527 198.76 1.02398
1061 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Subtracted High confidence 217.323 211.185 6.138
elks protein. [refseq;acc:nm_015064] Divided 218.162 211.648 1.03078
germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Low confidence 204.104 199.324 1.02398
tribbles homolog 2. [refseq;acc:nm_021643] Subtracted 203.515 198.787 4.728
1062 brain protein 44. [swissprot;acc:o95563] High confidence 126.215 120.078 6.137
dna-crosslink repair gene snm1. [refseq;acc:nm_014881] Divided Low confidence 203.048 198.295 1.02397
eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Subtracted 202.98 198.253 4.727
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Divided High confidence 269.963 278.239 1.03066
1063 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 126.215 120.078 6.137
t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] Divided Low confidence 203.048 198.295 1.02397
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Subtracted 196.475 191.748 4.727
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided High confidence 269.96 278.232 1.03064
1064 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] Subtracted 217.315 211.183 6.132
electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Low confidence 198.075 193.349 4.726
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 201.995 197.269 1.02396
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] High confidence 269.955 278.221 1.03062
1065 atp-binding cassette, sub-family f, member 2 (iron inhibited abc transporter 2) (hussy-18). [swissprot;acc:q9ug63] Low confidence 201.115 196.411 1.02395
septin 10 isoform 1. [refseq;acc:nm_144710] Subtracted High confidence 125.526 119.402 6.124
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Low confidence 201.995 197.269 4.726
zinc finger protein 305. [swissprot;acc:o43309] Divided High confidence 269.954 278.219 1.03062
1066 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 124.434 118.318 6.116
sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676] Low confidence 203.333 198.607 4.726
yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6] Divided 187.762 183.372 1.02394
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] High confidence 269.956 278.223 1.03062
1067 mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Subtracted 213.552 207.463 6.089
ubiquitin. [swissprot;acc:p02248] Low confidence 193.011 188.286 4.725
yippee-like protein 5. [swissprot;acc:q96ns1] Divided 187.77 183.38 1.02394

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/