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 3080 to 3129 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1540 pxr2b protein. [refseq;acc:nm_016559] Subtracted 6996.51 7429.18 432.67
1541 adenylyl cyclase-associated protein 1 (cap 1). [swissprot;acc:q01518] Divided 5989.3 6427.17 1.07311
dimeric dihydrodiol dehydrogenase; 3-deoxyglucosone reductase. [refseq;acc:nm_014475] Subtracted 6158.32 6590.99 432.67
1542 glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] 5686.74 6119.36 432.62
inositol polyphosphate multikinase. [refseq;acc:nm_152230] Divided 5466 5865.33 1.07306
1543 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Subtracted 6885.11 7317.48 432.37
afg3-like protein 2 (ec 3.4.24.-) (paraplegin-like protein). [swissprot;acc:q9y4w6] Divided 5466 5865.33 1.07306
1544 alpha-(1,6)-fucosyltransferase (ec 2.4.1.68) (glycoprotein 6-alpha-l- fucosyltransferase) (gdp-fucose--glycoprotein fucosyltransferase) (gdp-l-fuc:n-acetyl-beta-d-glucosaminide alpha1,6-fucosyltransferase) (alpha1-6fuct) (fucosyltransferase 8). [swissprot;acc:q9byc5]
hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Subtracted 5798.31 6230.55 432.24
1545 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Divided 5945.96 6380.28 1.07304
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Subtracted 5672.68 6104.68 432
1546 26s proteasome non-atpase regulatory subunit 3 (26s proteasome regulatory subunit s3) (proteasome subunit p58). [swissprot;acc:o43242] Divided 5819.39 6244.37 1.07303
e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Subtracted 5672.25 6104.01 431.76
1547 cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] Divided 5397.21 5790.45 1.07286
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Subtracted 5672.25 6104.01 431.76
1548 60s ribosomal protein l28. [swissprot;acc:p46779] Divided 5987.29 6423.52 1.07286
65 kda yes-associated protein (yap65). [swissprot;acc:p46937] Subtracted 5672.25 6104.01 431.76
1549 9 kda protein. [swissprot;acc:p13994]
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Divided 6025.86 6464.16 1.07274
1550 collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Subtracted 5672.23 6103.98 431.75
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Divided 6025.86 6464.16 1.07274
1551 cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007] 5732.83 6149.86
transcriptional co-activator with pdz-binding motif (taz). [refseq;acc:nm_015472] Subtracted 5672.24 6103.99 431.75
1552 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Divided 6025.86 6464.16 1.07274
collagen alpha 3(iv) chain precursor (goodpasture antigen). [swissprot;acc:q01955] Subtracted 5672.2 6103.92 431.72
1553 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Divided 5875.75 6302.76 1.07267
tensin. [refseq;acc:nm_022648] Subtracted 5871.89 6303.56 431.67
1554 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 6830.4 7261.98 431.58
prefoldin subunit 1. [swissprot;acc:o60925] Divided 5875.75 6302.76 1.07267
1555 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
zasp protein (fragment). [sptrembl;acc:q9y4z3] Subtracted 5671.93 6103.49 431.56
1556 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] 5869.97 6301.24 431.27
choline dehydrogenase. [refseq;acc:nm_018397] Divided 5875.75 6302.76 1.07267
1557 t-cell activation wd repeat protein. [refseq;acc:nm_139281] Subtracted 4062.03 4492.48 430.45
vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253] Divided 6018.7 6455.7 1.07261
1558 tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Subtracted 5870.72 6300.83 430.11
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Divided 6048.57 6487.65 1.07259
1559 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] Subtracted 4063.64 4492.98 429.34
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Divided 6048.57 6487.65 1.07259
1560 pbk1 protein. [sptrembl;acc:o76021] Subtracted 4064.23 4493.36 429.13
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Divided 6048.57 6487.65 1.07259
1561 dpy-30-like protein. [swissprot;acc:q9c005] Subtracted 5602.01 6031.05 429.04
vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269] Divided 6078.43 6519.6 1.07258
1562 adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123] 5984.88 6419.11 1.07255
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151] Subtracted 5602.01 6031.05 429.04
1563 gamma-snap-associated factor 1; rab11-interacting protein. [refseq;acc:nm_015470]
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Divided 6221.35 6672.51 1.07252
1564 neighbor of cox4. [swissprot;acc:o43402] Subtracted 5602.01 6031.05 429.04
proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] Divided 6257.62 6711.4 1.07252
1565 proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] 6343.76 6803.44 1.07246

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/