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 3132 to 3181 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
392 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Measured Subtracted 6251.91 7192.08 940.17
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 5921.4
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Ranked 239.092 257.705 18.613
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Squared Divided 28895.6 35572.8 1.23108
vav-3 protein. [swissprot;acc:q9ukw4] Rooted Subtracted 66.089 72.3555 6.2665
393 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared 26157.6 20236.2 5921.4
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Rooted Divided 49.8842 45.2875 1.1015
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Ranked Subtracted 238.921 257.327 18.406
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Measured Divided 4490.28 5222.25 1.16301
grancalcin. [swissprot;acc:p28676] Subtracted 6251.96 7192.13 940.17
spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834] Ranked Divided 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
vav-2 protein. [swissprot;acc:p52735] Rooted Subtracted 66.088 72.2597 6.1717
394 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared 26157.6 20236.2 5921.4
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Measured Divided 4490.28 5222.25 1.16301
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Ranked Subtracted 207.889 226.226 18.337
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Divided 218.827 238.407 1.08948
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Rooted Subtracted 58.0752 64.23 6.1548
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150] Measured 1834.33 895.134 939.196
mad protein (max dimerizer). [swissprot;acc:q05195] Squared Divided 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
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798] Measured Subtracted 1834.36 895.194 939.166
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared 26157.6 20236.2 5921.4
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Divided 17254.4 21218.1 1.22972
phosducin-like protein (phlp). [swissprot;acc:q13371] Ranked Subtracted 207.908 226.218 18.31
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Rooted Divided 50.0423 45.4523 1.10098
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted 58.0752 64.23 6.1548
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Measured Divided 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
dok-like protein. [refseq;acc:nm_024872] Subtracted 63.2134 69.352 6.1386
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared 26157.6 20236.2 5921.4
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08] Measured 1834.52 895.507 939.013
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Squared Divided 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
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] Subtracted 207.908 226.218 18.31
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Measured Divided 6563.65 7627.29 1.16205
397 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Rooted Subtracted 63.2134 69.352 6.1386
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670] Measured 1834.59 895.633 938.957
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 26157.6 20236.2 5921.4
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 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
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked Subtracted 207.908 226.218 18.31
t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Divided 110.689 101.613 1.08932
398 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Rooted Subtracted 63.2134 69.352 6.1386
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Measured 1834.63 895.697 938.933
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Squared Divided 18929.1 23222.8 1.22683
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Subtracted 26157.6 20236.2 5921.4
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked Divided 218.818 238.358 1.0893

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/