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 3180 to 3229 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1590 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
1607 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Divided 214.982 211.622 1.01588
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Subtracted 228.484 231.74 3.256
1608 g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 218.789 215.533
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] Divided 208.106 204.867 1.01581
1609 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Subtracted 207.916 204.662 3.254
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided 208.113 204.876 1.0158
1610 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 217.446 214.2 3.246
ubiquitin-conjugating enzyme e2 variant 2; 1 alpha,25-dihydroxyvitamin d3-inducible; enterocyte differentiation promoting factor; methyl methanesulfonate sensitive 2, s. cerevisiae, homolog of. [refseq;acc:nm_003350] Divided 208.122 204.886 1.01579
1611 p10-binding protein. [refseq;acc:nm_024491] 221.313 217.877 1.01577
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted 217.446 214.2 3.246
1612 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Divided 221.426 224.902 1.0157
pp1201 protein. [refseq;acc:nm_022152] Subtracted 217.446 214.2 3.246
1613 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Divided 182.378 185.241 1.0157
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 217.446 214.2 3.246
1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] Divided 217.233 213.897 1.0156
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted 217.446 214.2 3.246
1615 dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] Divided 246.38 242.596 1.0156

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/