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 10764 to 10813 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2691 zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Rooted 44.585 44.4412 1.00324
2692 aquaporin 5. [swissprot;acc:p55064] Ranked 188.192 188.048 1.00077
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Squared 22249 22757.3 1.02285
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] Measured 4113.79 4095.53 1.00446
sin3 associated polypeptide p18 (2hor0202). [swissprot;acc:o00422] Rooted 65.5664 65.7788 1.00324
2693 e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040] Measured 4113.79 4095.53 1.00446
hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Squared 22249 22757.3 1.02285
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Ranked 188.193 188.049 1.00077
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Rooted 44.5853 44.4416 1.00323
2694 60s ribosomal protein l18. [swissprot;acc:q07020] Measured 4113.79 4095.53 1.00446
aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Ranked 188.223 188.081 1.00075
cgthba protein (-14 gene protein). [swissprot;acc:q12980] Squared 22249 22757.3 1.02285
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Rooted 44.585 44.4413 1.00323
2695 endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Measured 5176.92 5154.43 1.00436
hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Squared 22249 22757.3 1.02285
signal recognition particle 54 kda protein (srp54). [swissprot;acc:p13624] Ranked 215.545 215.384 1.00075
zinc finger protein 274 (zinc finger protein sp2114) (zinc finger protein hfb101) (zinc finger protein zfp2) (zf2). [swissprot;acc:q96gc6] Rooted 44.5865 44.4436 1.00322
2696 iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] Ranked 201.652 201.794 1.0007
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Squared 7758.36 7593.09 1.02177
programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831] Measured 5176.92 5154.43 1.00436
zinc finger protein 232. [swissprot;acc:q9uny5] Rooted 44.5859 44.4426 1.00322
2697 arp2/3 complex 34 kda subunit (p34-arc) (actin-related protein 2/3 complex subunit 2). [swissprot;acc:o15144] Ranked 225.081 225.232 1.00067
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Squared 7773.43 7608.56 1.02167
t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947] Measured 5176.92 5154.43 1.00436
zinc finger protein 99. [refseq;acc:nm_032164] Rooted 44.586 44.4429 1.00322
2698 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Squared 29695.1 30338.4 1.02166
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Ranked 188.435 188.31 1.00066
trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] Measured 4163.36 4145.95 1.0042
zinc finger protein 305. [swissprot;acc:o43309] Rooted 44.5858 44.4426 1.00322
2699 calsyntenin-1 precursor. [swissprot;acc:o94985] Ranked 188.435 188.31 1.00066
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Measured 5356.83 5378.19 1.00399
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Squared 7777.03 7612.25 1.02165
zinc finger protein 213 (putative transcription factor cr53). [swissprot;acc:o14771] Rooted 44.5861 44.443 1.00322
2700 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 65.3323 65.1252 1.00318
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Squared 7788.59 7624.11 1.02157
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Measured 5239.33 5260 1.00395
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Ranked 188.435 188.31 1.00066
2701 dynein light chain 2. [refseq;acc:nm_080677] Measured 5239.33 5260 1.00395
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Squared 31182.7 31851.7 1.02145
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Rooted 65.5656 65.768 1.00309
serine/threonine-protein kinase dcamkl1 (ec 2.7.1.-) (doublecortin- like and cam kinase-like 1). [swissprot;acc:o15075] Ranked 216.539 216.682 1.00066
2702 creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Measured 8971.66 9006.92 1.00393
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Ranked 188.435 188.311 1.00066
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Squared 31182.7 31851.7 1.02145
zinc finger protein 444; endothelial zinc finger protein 2. [refseq;acc:nm_018337] Rooted 44.6114 44.4835 1.00288
2703 creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Measured 8972.87 9007.71 1.00388
integral membrane protein cii-3b. [sptrembl;acc:o75609] Rooted 65.6868 65.5154 1.00262
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Squared 31182.7 31851.7 1.02145
thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7] Ranked 188.435 188.311 1.00066
2704 creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732] Measured 8980.12 9013.33 1.0037

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/