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 2962 to 3011 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1481 egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 3688.8 3431.33 1.07504
1482 leng5 protein. [refseq;acc:nm_024075] 5372.25 5775.21 1.07501
ubiquitin. [swissprot;acc:p02248] Subtracted 6158.22 6597.55 439.33
1483 tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 6048.57 6487.65 439.08
1484 ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 6048.57 6487.65 439.08
1485 tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] Divided 5372.25 5775.21 1.07501
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 6048.57 6487.65 439.08
1486 p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] 7210.87 7649.23 438.36
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Divided 5372.25 5775.21 1.07501
1487 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Subtracted 6025.86 6464.16 438.3
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Divided 5573.64 5991.58 1.07499
1488 delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886]
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Subtracted 6025.86 6464.16 438.3
1489 general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] 7210.64 7648.94
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Divided 6192.38 6656.34 1.07492
1490 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Subtracted 6025.86 6464.16 438.3
f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] Divided 6340.5 6815.41 1.0749
1491 26s protease regulatory subunit 4 (p26s4). [swissprot;acc:q03527] Subtracted 5938.56 6376.76 438.2
fidgetin-like 1. [refseq;acc:nm_022116] Divided 6057.46 6510.9 1.07486
1492 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Subtracted 5989.3 6427.17 437.87
dna replication licensing factor mcm3 (dna polymerase alpha holoenzyme-associated protein p1) (rlf beta subunit) (p102 protein) (p1-mcm3). [swissprot;acc:p25205] Divided 4619.81 4965.45 1.07482
1493 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 6606.21
zinc finger protein zic 1 (zinc finger protein of the cerebellum 1). [swissprot;acc:q15915] Subtracted 5658.51 6096.21 437.7
1494 kelch-like ech-associated protein 1 (cytosolic inhibitor of nrf2). [swissprot;acc:q14145] Divided 4619.81 4965.45 1.07482
zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481] Subtracted 5658.55 6095.85 437.3
1495 nadh-ubiquinone oxidoreductase pdsw subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-pdsw) (ci-pdsw). [swissprot;acc:o96000] Divided 6362.92 6838.6 1.07476
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Subtracted 5401.39 5838.63 437.24
1496 apoptosis-inducing factor (aif)-homologous mitochondrion-associated inducer of death; p53-responsive gene 3. [refseq;acc:nm_032797] Divided 5945.56 6389.63 1.07469
transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] Subtracted 7195.76 7632.83 437.07
1497 f-actin capping protein alpha-2 subunit (capz alpha-2). [swissprot;acc:p47755] Divided 6339.08 6812.45 1.07467
zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409] Subtracted 5658.58 6095.62 437.04
1498 40s ribosomal protein s13. [swissprot;acc:q02546] Divided 5414.98 5818.7 1.07456
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Subtracted 6018.7 6455.7 437
1499 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 5798.31 6230.55 1.07455
importin 4. [refseq;acc:nm_024658] Subtracted 5613.16 6050.16 437
1500 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Divided 10075.5 9377.75 1.0744
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Subtracted 4846.16 5283.08 436.92
1501 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Divided 10075.5 9377.75 1.0744
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2] Subtracted 5132.68 5569.54 436.86
1502 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Divided 10075.5 9377.75 1.0744
proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786] Subtracted 6068.03 6504.59 436.56
1503 60s ribosomal protein l28. [swissprot;acc:p46779] 5987.29 6423.52 436.23
coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Divided 10075.5 9377.75 1.0744
1504 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9]
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Subtracted 6326.24 6762.27 436.03
1505 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Divided 10075.5 9377.75 1.0744
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Subtracted 6326.24 6762.27 436.03
1506 dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690]

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/