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 1562 to 1611 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
391 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared 28895.6 35572.8 1.23108
protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378] Rooted 50.3345 45.6718 1.10209
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Measured 3658.76 3144.39 1.16358
392 60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Ranked 241.83 263.615 1.09008
60s ribosomal protein l3-like. [swissprot;acc:q92901] Rooted 50.3313 45.6913 1.10155
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072] Measured 3641.89 4236.95 1.16339
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared 28895.6 35572.8 1.23108
393 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Rooted 49.8842 45.2875 1.1015
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Measured 4490.28 5222.25 1.16301
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked 225.719 207.072 1.09005
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Squared 28895.6 35572.8 1.23108
394 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured 4490.28 5222.25 1.16301
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Ranked 218.827 238.407 1.08948
mad protein (max dimerizer). [swissprot;acc:q05195] Squared 17248.4 21214 1.22991
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Rooted 58.6533 64.5958 1.10132
395 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked 218.827 238.407 1.08948
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Squared 17254.4 21218.1 1.22972
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Rooted 50.0423 45.4523 1.10098
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Measured 4532.73 5269.33 1.16251
396 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted 116.797 106.111 1.10071
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Squared 17256.5 21219.6 1.22966
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] Ranked 240.801 262.34 1.08945
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Measured 6563.65 7627.29 1.16205
397 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Squared 17257.5 21220.3 1.22963
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Measured 5367.04 6233.12 1.16137
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Rooted 116.792 106.107 1.1007
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Ranked 110.689 101.613 1.08932
398 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Squared 18929.1 23222.8 1.22683
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked 218.818 238.358 1.0893
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Rooted 116.707 106.044 1.10055
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Measured 5084.26 5904.1 1.16125
399 clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked 207.889 226.226 1.08821
cyclin g2. [swissprot;acc:q16589] Rooted 116.707 106.044 1.10055
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Squared 18929.1 23222.8 1.22683
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Measured 5201.41 4479.76 1.16109
400 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
cyclin g1 (cyclin g). [swissprot;acc:p51959] Rooted 116.707 106.044 1.10055
glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Squared 39478.8 48419 1.22646
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked 207.908 226.218 1.08807
401 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Measured 5201.41 4479.76 1.16109
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Squared 33044.3 40524.8 1.22638
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Ranked 207.908 226.218 1.08807
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Rooted 116.707 106.044 1.10055
402 endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Squared 39472 48393.1 1.22601
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 1.10037
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Measured 5201.41 4479.76 1.16109
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 207.908 226.218 1.08807
403 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Measured 5201.41 4479.76 1.16109
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Squared 39463.9 48362.1 1.22548
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 59.6834 65.6741 1.10037

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/