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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6408 to 6457 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1602 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided High confidence 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
putative atp-dependent clp protease proteolytic subunit, mitochondrial precursor (ec 3.4.21.92) (endopeptidase clp). [swissprot;acc:q16740] Low confidence 204.216 200.037 1.02089
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Subtracted 152.572 148.47 4.102
1604 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] Divided 204.216 200.037 1.02089
inhibitor of nuclear factor kappa-b kinase epsilon subunit (ec 2.7.1.-) (i kappa-b kinase epsilon) (ikbke) (ikk-epsilon) (ikk-e) (inducible i kappa-b kinase) (ikk-i). [swissprot;acc:q14164] Subtracted 204.39 200.288 4.102
mitotic checkpoint protein bub3. [swissprot;acc:o43684] High confidence 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 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] Subtracted Low confidence 201.291 197.189 4.102
dual specificity protein phosphatase 15 (ec 3.1.3.48) (ec 3.1.3.16). [swissprot;acc:q9h1r2] Divided 199.691 195.607 1.02088
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] High confidence 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
delta-interacting protein a (hepatitis delta antigen interacting protein a). [swissprot;acc:q15834] Subtracted Low confidence 201.993 197.894 4.099
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Divided 204.475 200.292 1.02088
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Subtracted High confidence 228.477 231.747 3.27
1607 dual specificity protein phosphatase 5 (ec 3.1.3.48) (ec 3.1.3.16) (dual specificity protein phosphatase hvh3). [swissprot;acc:q16690] Divided Low confidence 199.691 195.607 1.02088
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] High confidence 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
transketolase (ec 2.2.1.1) (tk). [swissprot;acc:p29401] Low confidence 201.817 197.718 4.099
1608 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Divided 199.691 195.607 1.02088
ctf18, chromosome transmission fidelity factor 18 homolog; homolog of yeast chl12. [refseq;acc:nm_022092] Subtracted 200.714 196.617 4.097
g1 to s phase transition protein 1 homolog (gtp-binding protein gst1-hs). [swissprot;acc:p15170] High confidence 218.789 215.533 3.256
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
dual specificity protein phosphatase 13 (ec 3.1.3.48) (ec 3.1.3.16) (testis- and skeletal-muscle-specific dsp). [swissprot;acc:q9uii6] Divided Low confidence 199.691 195.607 1.02088
homeobox protein hox-c8 (hox-3a). [swissprot;acc:p31273] Subtracted 203.127 199.033 4.094
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] Divided High confidence 208.113 204.876 1.0158
1610 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Subtracted 217.446 214.2 3.246
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Low confidence 185.205 181.112 4.093
mus81 endonuclease. [refseq;acc:nm_025128] Divided 195.31 191.317 1.02087
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] High confidence 208.122 204.886 1.01579
1611 hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819] Subtracted Low confidence 197.747 193.656 4.091
p10-binding protein. [refseq;acc:nm_024491] Divided High confidence 221.313 217.877 1.01577
similar to hepatocellular carcinoma-associated antigen hca557b. [refseq;acc:nm_145280] Low confidence 195.31 191.317 1.02087
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Subtracted High confidence 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
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 195.31 191.317 1.02087
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Subtracted 197.752 193.661 4.091
pp1201 protein. [refseq;acc:nm_022152] High confidence 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
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Subtracted Low confidence 197.74 193.65 4.09
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] High confidence 217.446 214.2 3.246
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] Divided Low confidence 192.787 188.847 1.02086
1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] High confidence 217.233 213.897 1.0156
ras-related protein rap-2b. [swissprot;acc:p17964] Low confidence 202.026 197.9 1.02085
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Subtracted High confidence 217.446 214.2 3.246
zinc finger-like protein 9. [refseq;acc:nm_033414] Low confidence 202.494 198.406 4.088
1615 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] Divided 205.179 200.988 1.02085

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/