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 1510 to 1559 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
189 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Ranked Divided 226.582 198.444 1.14179
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared Subtracted 70694.1 56989.9 13704.2
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Rooted Divided 46.0352 53.0192 1.15171
190 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Squared 71389.9 96037.6 1.34525
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Measured 4571.89 5864.86 1.28281
fad synthetase. [refseq;acc:nm_025207] Ranked Subtracted 241.373 267.352 25.979
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Rooted Divided 149.165 129.699 1.15009
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Squared Subtracted 42411.6 55802.1 13390.5
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] Rooted 47.6504 36.9304 10.72
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Measured 4366.44 5899.76 1533.32
Ranked Divided 226.582 198.444 1.14179
191 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Rooted Subtracted 116.797 106.111 10.686
aquaporin 5. [swissprot;acc:p55064] Squared Divided 71388.5 96035.2 1.34525
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Ranked Subtracted 241.373 267.352 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Measured 4366.44 5899.76 1533.32
Ranked Divided 226.582 198.444 1.14179
pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] Rooted 63.1192 72.584 1.14995
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Squared Subtracted 42411.6 55802.1 13390.5
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Measured Divided 4638.1 5923.4 1.27712
192 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] 17757.5 14008 1.26767
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Squared 71387.4 96033.4 1.34524
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked Subtracted 241.373 267.352 25.979
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 199.458 1.14055
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Rooted Subtracted 116.792 106.107 10.685
small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Measured 10807.4 12338.5 1531.1
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Rooted Divided 53.6107 61.5862 1.14877
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared Subtracted 42411.6 55802.1 13390.5
193 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Ranked 241.373 267.352 25.979
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Squared Divided 71386.9 96032.5 1.34524
musashi 1. [refseq;acc:nm_002442] Ranked 227.491 199.458 1.14055
nostrin. [refseq;acc:nm_052946] Rooted 59.6399 51.9242 1.1486
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Measured 17756.5 14007.3 1.26766
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared Subtracted 42411.6 55802.1 13390.5
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 10.663
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Measured 4612.39 3093.6 1518.79
194 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Squared Divided 71346.6 95965.1 1.34505
cyclin g2. [swissprot;acc:q16589] Measured 17738.6 13995.7 1.26743
Rooted Subtracted 116.707 106.044 10.663
eap30 subunit of ell complex. [refseq;acc:nm_007241] Divided 59.6399 51.9242 1.1486
huntingtin interacting protein c. [refseq;acc:nm_012272] Measured Subtracted 4300.47 5807.72 1507.25
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared 42411.6 55802.1 13390.5
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Ranked 241.373 267.352 25.979
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 227.491 199.458 1.14055
195 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Subtracted 241.373 267.352 25.979
cyclin g1 (cyclin g). [swissprot;acc:p51959] Measured Divided 17738.5 13995.6 1.26743
Rooted Subtracted 116.707 106.044 10.663
huntingtin interacting protein c. [refseq;acc:nm_012272] Ranked Divided 227.971 200.417 1.13748
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Rooted 59.6399 51.9242 1.1486
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Squared Subtracted 42411.6 55802.1 13390.5
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Measured 3074.57 4567.51 1492.94

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/