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 2101 to 2150 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1051 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] High confidence 211.449 217.998 1.03097
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Low confidence 200.439 205.267 1.02409
1052 retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] High confidence 211.449 217.998 1.03097
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Low confidence 200.439 205.267 1.02409
1053 c-mpl binding protein. [refseq;acc:nm_052879] 204.184 199.387 1.02406
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] High confidence 207.04 200.84 1.03087
1054 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Low confidence 210.793 205.841 1.02406
1055 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] High confidence 219.01 212.468 1.03079
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Low confidence 199.656 194.966 1.02406
1056 phenylalanine-trna synthetase. [refseq;acc:nm_006567] 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]
phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] 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
1059 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 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
1060 nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] High confidence 218.162 211.648 1.03078
synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Low confidence 203.527 198.76 1.02398
1061 elks protein. [refseq;acc:nm_015064] High confidence 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
1062 dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 203.048 198.295 1.02397
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] High confidence 269.963 278.239 1.03066
1063 t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] Low confidence 203.048 198.295 1.02397
zinc finger imprinted 2. [swissprot;acc:q9nzv7] High confidence 269.96 278.232 1.03064
1064 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 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
zinc finger protein 305. [swissprot;acc:o43309] High confidence 269.954 278.219 1.03062
1066 yippee-like protein 2 (digeorge syndrome-related protein fksg4). [swissprot;acc:q96qa6] Low confidence 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 yippee-like protein 5. [swissprot;acc:q96ns1] Low confidence 187.77 183.38 1.02394
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] High confidence 269.956 278.223 1.03062
1068 disrupter of silencing 10. [refseq;acc:nm_020368] Low confidence 199.958 195.283 1.02394
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] High confidence 269.953 278.215 1.03061
1069 yippee-like protein 3 (digeorge syndrome-related protein fksg5). [swissprot;acc:q9bsj4] Low confidence 187.761 183.371 1.02394
zinc finger protein 232. [swissprot;acc:q9uny5] High confidence 269.954 278.218 1.03061
1070 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Low confidence 203.828 199.067 1.02392
zinc finger protein 99. [refseq;acc:nm_032164] High confidence 269.954 278.218 1.03061
1071 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 238.356
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Low confidence 200.19 195.515 1.02391
1072 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 203.286 198.543 1.02389
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] High confidence 269.954 278.217 1.03061
1073 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Low confidence 210.723 205.809 1.02388
ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9] High confidence 216.901 210.485 1.03048
1074 adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Low confidence 191.57 187.103 1.02387
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] High confidence 174.387 179.697 1.03045
1075 adenosine deaminase (ec 3.5.4.4) (adenosine aminohydrolase). [swissprot;acc:p00813] Low confidence 202.317 197.601 1.02387
coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] High confidence 174.387 179.697 1.03045

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/