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 4858 to 4907 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1215 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Ranked 218.268 212.916 1.02514
mitotic checkpoint protein bub3. [swissprot;acc:o43684] Rooted 60.2183 62.9735 1.04575
nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Squared 20823.1 23668.4 1.13664
1216 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 20823.5 23668.7 1.13663
fibulin-2 precursor. [swissprot;acc:p98095] Measured 8670.59 9412.9 1.08561
retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Ranked 218.269 212.918 1.02513
zinc finger protein 207. [swissprot;acc:o43670] Rooted 60.2183 62.9735 1.04575
1217 cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [swissprot;acc:p27708] Measured 6021.21 6536.45 1.08557
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Rooted 61.4717 64.2826 1.04573
gdp-mannose pyrophosphorylase b isoform 1; mannose-1-phosphate guanylyltransferase; amphoterin induced gene 3. [refseq;acc:nm_013334] Squared 22101.6 25118.6 1.13651
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Ranked 211.959 217.258 1.025
1218 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] Measured 5736 6226.52 1.08552
fatty-acid amide hydrolase (ec 3.1.-.-) (oleamide hydrolase) (anandamide amidohydrolase). [swissprot;acc:o00519] Ranked 211.959 217.258 1.025
gdp-mannose pyrophosphorylase a; mannose-1-phosphate guanylyltransferase (gdp). [refseq;acc:nm_013335] Squared 22101.6 25118.6 1.13651
hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Rooted 51.9837 54.3601 1.04571
1219 coactosin-like protein. [swissprot;acc:q14019] Ranked 211.959 217.258 1.025
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Rooted 61.4767 64.2857 1.04569
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Squared 20836.6 23679.5 1.13644
tcd37 homolog; prune. [refseq;acc:nm_021222] Measured 5735.95 6226.46 1.08552
1220 40s ribosomal protein s3a. [swissprot;acc:p49241] Squared 19516.8 22178 1.13635
cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Measured 5735.65 6226.13 1.08551
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Rooted 58.0178 60.6658 1.04564
uracil-dna glycosylase, mitochondrial precursor (ec 3.2.2.-) (udg). [swissprot;acc:p13051] Ranked 211.959 217.258 1.025
1221 casein kinase i alpha s-like. [refseq;acc:nm_145203] Squared 20055.2 22788 1.13626
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] Measured 5736.34 6226.88 1.08551
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Rooted 66.3775 69.4004 1.04554
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Ranked 211.959 217.258 1.025
1222 casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] Squared 20055.2 22788 1.13626
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] Measured 5735.74 6226.23 1.08551
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Rooted 66.3775 69.4004 1.04554
tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890] Ranked 206.774 211.936 1.02496
1223 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Squared 22572.2 25647.6 1.13625
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Rooted 62.2596 65.0928 1.04551
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Measured 6011.44 6524.55 1.08536
tumor protein d52 (n8 protein). [swissprot;acc:p55327] Ranked 206.771 211.926 1.02493
1224 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] Squared 27558.3 31303.1 1.13589
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Ranked 225.906 231.524 1.02487
hskin17 protein. [refseq;acc:nm_012311] Rooted 62.2596 65.0928 1.04551
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Measured 4331.35 4700.91 1.08532
1225 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 5546.5 6019.57 1.08529
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Rooted 62.2596 65.0928 1.04551
protein-tyrosine phosphatase, non-receptor type 2 (ec 3.1.3.48) (t- cell protein-tyrosine phosphatase) (tcptp). [swissprot;acc:p17706] Squared 27784.4 31556.6 1.13577
ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] Ranked 166.846 170.989 1.02483
1226 polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Rooted 62.2596 65.0928 1.04551
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Squared 27802.5 31577 1.13576
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Measured 5997.24 6508.62 1.08527
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] Ranked 166.846 170.989 1.02483
1227 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Squared 19620.8 22280.7 1.13557
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Measured 5973.95 6483.32 1.08527
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Rooted 62.2596 65.0928 1.04551

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/