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 3208 to 3257 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
401 transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 0 12305.9 11904.9 1.03368
402 actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Rooted 21.6987 22.4088 1.03273
adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5] Ranked 10562.4 10918 1.03367
brain protein 16. [refseq;acc:nm_016458] Squared 2538.95 2371.77 1.07049
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 1 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
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 0 548.5 527.5 1.03981
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Ranked 1 207.908 226.218 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
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 1872.12 1754.91 1.06679
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Measured 548.5 527.5 1.03981
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Rooted 1 59.6834 65.6741 1.10037
phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941] Ranked 207.908 226.218 1.08807
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Rooted 0 19.4322 20.0671 1.03267
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] Ranked 9783.63 10111.2 1.03348
404 40s ribosomal protein s3a. [swissprot;acc:p49241] Rooted 34.0198 32.9781 1.03159
adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Squared 1 26819.1 32855.4 1.22507
dna repair protein rad52 homolog. [swissprot;acc:p43351] Ranked 207.908 226.218 1.08807
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Measured 5201.41 4479.76 1.16109
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Rooted 59.6834 65.6741 1.10037
thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Measured 0 1229.57 1278.36 1.03968
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Squared 84448.4 89963.1 1.0653
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] Ranked 9783.63 10111.2 1.03348
405 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Squared 1 26822.2 32858.1 1.22503
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Rooted 116.576 105.948 1.10031
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Ranked 207.931 226.209 1.0879
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Squared 0 84951.4 90481 1.06509
integral membrane protein cii-3b. [sptrembl;acc:o75609] Measured 2218.63 2304.22 1.03858
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 1 5201.41 4479.76 1.16109
survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] Rooted 0 17.5059 16.9709 1.03152
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] Ranked 9783.63 10111.2 1.03348
406 60s ribosomal protein l12. [swissprot;acc:p30050] Rooted 1 49.9858 45.4433 1.09996
fibrillin 3. [refseq;acc:nm_032447] Squared 0 48035.2 45133.4 1.06429
glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075] Ranked 9783.63 10111.2 1.03348
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Squared 1 18995.7 23245.6 1.22373
thymic stromal co-transporter. [refseq;acc:nm_033051] Measured 5201.41 4479.76 1.16109
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked 265.634 244.304 1.08731
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Rooted 0 44.9117 43.5558 1.03113
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured 2363.32 2454.04 1.03839
407 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Ranked 1 239.75 260.544 1.08673
60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Rooted 49.9856 45.4431 1.09996
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Squared 0 192242 204096 1.06166
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Measured 3614.24 3481.87 1.03802
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Rooted 6.9282 7.14143 1.03078
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Squared 1 18995.7 23244.9 1.22369
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] Ranked 0 9783.63 10111.2 1.03348
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Measured 1 6603.41 7664.65 1.16071
408 ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Ranked 255.112 234.804 1.08649

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/