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 3163 to 3212 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1582 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Divided 168.098 170.844 1.01634
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Subtracted 227.768 231.246 3.478
1583 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Divided 168.091 170.837 1.01634
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Subtracted 227.768 231.246 3.478
1584 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 216.891 220.432 1.01633
enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Subtracted 221.426 224.902 3.476
1585 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Divided 168.145 170.888 1.01631
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Subtracted 217.871 214.404 3.467
1586 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] Divided 222.166 225.79 1.01631
rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Subtracted 230.643 227.194 3.449
1587 cda11 protein. [refseq;acc:nm_032026] 213.181 209.732
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Divided 220.129 216.598 1.0163
1588 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Subtracted 181.882 178.438 3.444
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Divided 177.834 180.725 1.01626
1589 p10-binding protein. [refseq;acc:nm_024491] Subtracted 221.313 217.877 3.436
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Divided 223.589 227.219 1.01624
1590 n-acetylglutamate synthase. [refseq;acc:nm_153006] Subtracted 223.179 226.611 3.432
thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Divided 225.119 228.769 1.01621
1591 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Subtracted 217.268 213.842 3.426
1592 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Divided 225.119 228.769 1.01621
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Subtracted 228.611 225.185 3.426
1593 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Divided 225.119 228.769 1.01621
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Subtracted 228.611 225.185 3.426
1594 adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] Divided 222.133 225.731 1.0162
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769] Subtracted 228.611 225.185 3.426
1595 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] Divided 222.134 225.731 1.01619
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345] Subtracted 228.611 225.185 3.426
1596 adapter-related protein complex 1 gamma 1 subunit (gamma-adaptin) (adaptor protein complex ap-1 gamma-1 subunit) (golgi adaptor ha1/ap1 adaptin gamma-1 subunit) (clathrin assembly protein complex 1 gamma-1 large chain). [swissprot;acc:o43747] Divided 222.134 225.731 1.01619
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 217.334 213.914 3.42
1597 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] Divided 222.134 225.731 1.01619
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Subtracted 217.322 213.916 3.406
1598 adapter-related protein complex 1 sigma 1a subunit (sigma-adaptin 1a) (adaptor protein complex ap-1 sigma-1a subunit) (golgi adaptor ha1/ap1 adaptin sigma-1a subunit) (clathrin assembly protein complex 1 sigma- 1a small chain) (clathrin coat assembly protein ap19) (ha1 19 kda subunit) (sigma 1a subunit of ap-1 clathrin). [swissprot;acc:q00382] Divided 222.134 225.731 1.01619
heat shock factor binding protein 1. [swissprot;acc:o75506] Subtracted 216.62 213.22 3.4
1599 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Divided 217.871 214.404 1.01617
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Subtracted 214.984 211.614 3.37
1600 adapter-related protein complex 2 beta 1 subunit (beta-adaptin) (plasma membrane adaptor ha2/ap2 adaptin beta subunit) (clathrin assembly protein complex 2 beta large chain) (ap105b). [swissprot;acc:p21851] Divided 222.103 225.675 1.01608
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Subtracted 214.982 211.622 3.36
1601 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Divided 217.268 213.842 1.01602
serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] Subtracted 221.045 217.699 3.346
1602 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 217.233 213.897 3.336
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided 217.334 213.914 1.01599
1603 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Subtracted 228.654 231.933 3.279
heat shock factor binding protein 1. [swissprot;acc:o75506] Divided 216.62 213.22 1.01595
1604 mitotic checkpoint protein bub3. [swissprot;acc:o43684] Subtracted 221.934 218.658 3.276
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Divided 214.984 211.614 1.01593
1605 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 217.322 213.916 1.01592
zinc finger protein 207. [swissprot;acc:o43670] Subtracted 221.934 218.658 3.276
1606 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Divided 207.916 204.662 1.0159
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Subtracted 228.477 231.747 3.27

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/