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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Gene Rank Network Comparison Type description Value Type green Interaction Map Filtered network_comparison red
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
green
network_comparison
red
1590 Subtracted n-acetylglutamate synthase. [refseq;acc:nm_153006] 226.611 3.432 223.179
1591 Divided dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 228.769 1.01621 225.119
Subtracted phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 213.842 3.426 217.268
1592 Divided stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] 228.769 1.01621 225.119
Subtracted transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 225.185 3.426 228.611
1593 Divided stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] 228.769 1.01621 225.119
Subtracted thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] 225.185 3.426 228.611
1594 Divided adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] 225.731 1.0162 222.133
Subtracted 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] 225.185 3.426 228.611
1595 Divided 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] 225.731 1.01619 222.134
Subtracted 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] 225.185 3.426 228.611
1596 Divided 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] 225.731 1.01619 222.134
Subtracted phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 213.914 3.42 217.334
1597 Divided 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] 225.731 1.01619 222.134
Subtracted hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 213.916 3.406 217.322
1598 Divided 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] 225.731 1.01619 222.134
Subtracted heat shock factor binding protein 1. [swissprot;acc:o75506] 213.22 3.4 216.62
1599 Divided dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 214.404 1.01617 217.871
Subtracted protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 211.614 3.37 214.984
1600 Divided 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] 225.675 1.01608 222.103
Subtracted protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 211.622 3.36 214.982
1601 Divided phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] 213.842 1.01602 217.268
Subtracted serine hydroxymethyltransferase, cytosolic (ec 2.1.2.1) (serine methylase) (glycine hydroxymethyltransferase) (shmt). [swissprot;acc:p34896] 217.699 3.346 221.045
1602 Divided phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 213.914 1.01599 217.334
Subtracted hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 213.897 3.336 217.233
1603 Divided heat shock factor binding protein 1. [swissprot;acc:o75506] 213.22 1.01595 216.62
Subtracted early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 231.933 3.279 228.654
1604 Divided protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] 211.614 1.01593 214.984
Subtracted mitotic checkpoint protein bub3. [swissprot;acc:o43684] 218.658 3.276 221.934
1605 Divided hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 213.916 1.01592 217.322
Subtracted zinc finger protein 207. [swissprot;acc:o43670] 218.658 3.276 221.934
1606 Divided apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 204.662 1.0159 207.916
Subtracted transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] 231.747 3.27 228.477
1607 Divided protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] 211.622 1.01588 214.982
Subtracted transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 231.74 3.256 228.484
1608 Divided ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] 204.867 1.01581 208.106
Subtracted g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] 215.533 3.256 218.789
1609 Divided utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] 204.876 1.0158 208.113
Subtracted apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 204.662 3.254 207.916
1610 Divided 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] 204.886 1.01579 208.122
Subtracted c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 214.2 3.246 217.446
1611 Divided p10-binding protein. [refseq;acc:nm_024491] 217.877 1.01577 221.313
Subtracted z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] 214.2 3.246 217.446
1612 Divided enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] 224.902 1.0157 221.426
Subtracted pp1201 protein. [refseq;acc:nm_022152] 214.2 3.246 217.446
1613 Divided 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] 185.241 1.0157 182.378
Subtracted lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 214.2 3.246 217.446
1614 Divided hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 213.897 1.0156 217.233
Subtracted sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 214.2 3.246 217.446
1615 Divided dna polymerase epsilon subunit b (ec 2.7.7.7) (dna polymerase ii subunit b). [swissprot;acc:p56282] 242.596 1.0156 246.38

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/