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 Value Type description Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 3180 to 3229 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1590 thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] High confidence 225.119 228.769 1.01621
1591 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Low confidence 193.407 189.426 1.02102
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] High confidence 225.119 228.769 1.01621
1592 cysteine and histidine-rich domain (chord)-containing, zinc binding protein 1; chord domain-containing protein 1; cysteine and histidine-rich domain (chord)-containing, zinc-binding protein 1. [refseq;acc:nm_012124] Low confidence 206.658 202.403 1.02102
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] High confidence 225.119 228.769 1.01621
1593 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Low confidence 208.892 213.282 1.02102
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] High confidence 225.119 228.769 1.01621
1594 40s ribosomal protein s7 (s8). [swissprot;acc:p23821] Low confidence 205.505 201.279 1.021
adapter-related protein complex 1 gamma 2 subunit (gamma2-adaptin) (adaptor protein complex ap-1 gamma-2 subunit) (g2ad). [swissprot;acc:o75843] High confidence 222.133 225.731 1.0162
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] 222.134 1.01619
nuclear lim interactor-interacting factor 3 (nli-interacting factor 3) (nli-if). [swissprot;acc:q9gzu7] Low confidence 201.589 197.442 1.021
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] High confidence 222.134 225.731 1.01619
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Low confidence 205.496 201.273 1.02098
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] High confidence 222.134 225.731 1.01619
dna mismatch repair protein msh2. [swissprot;acc:p43246] Low confidence 201.786 197.643 1.02096
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] High confidence 222.134 225.731 1.01619
flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748] Low confidence 201.174 197.046 1.02095
1599 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] High confidence 217.871 214.404 1.01617
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989] Low confidence 201.174 197.046 1.02095
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] High confidence 222.103 225.675 1.01608
aldehyde oxidase (ec 1.2.3.1). [swissprot;acc:q06278] Low confidence 201.174 197.046 1.02095
1601 cg10958-like. [refseq;acc:nm_145038] 197.185 193.141 1.02094
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] High confidence 217.268 213.842 1.01602
1602 a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588] Low confidence 206.235 202.009 1.02092
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] High confidence 217.334 213.914 1.01599
1603 heat shock factor binding protein 1. [swissprot;acc:o75506] 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
1604 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] High confidence 214.984 211.614 1.01593
1605 dual specificity protein phosphatase 15 (ec 3.1.3.48) (ec 3.1.3.16). [swissprot;acc:q9h1r2] Low confidence 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
1606 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] 207.916 204.662 1.0159
dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] Low confidence 204.475 200.292 1.02088
1607 dual specificity protein phosphatase 5 (ec 3.1.3.48) (ec 3.1.3.16) (dual specificity protein phosphatase hvh3). [swissprot;acc:q16690] 199.691 195.607
protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] High confidence 214.982 211.622 1.01588
1608 adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Low confidence 199.691 195.607 1.02088
ubiquitin-conjugating enzyme e2 variant 1 isoform b; dna-binding protein. [refseq;acc:nm_003349] High confidence 208.106 204.867 1.01581
1609 dual specificity protein phosphatase 13 (ec 3.1.3.48) (ec 3.1.3.16) (testis- and skeletal-muscle-specific dsp). [swissprot;acc:q9uii6] Low confidence 199.691 195.607 1.02088
utp--glucose-1-phosphate uridylyltransferase 2 (ec 2.7.7.9) (udp- glucose pyrophosphorylase 2) (udpgp 2) (ugpase 2). [swissprot;acc:q16851] High confidence 208.113 204.876 1.0158
1610 mus81 endonuclease. [refseq;acc:nm_025128] Low confidence 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 p10-binding protein. [refseq;acc:nm_024491] 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
1612 enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] High confidence 221.426 224.902 1.0157
hepatocellularcarcinoma-associated antigen hca557a. [refseq;acc:nm_015433] Low confidence 195.31 191.317 1.02087
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] High confidence 182.378 185.241 1.0157
mitochondrial gtp binding protein isoform v. [refseq;acc:nm_032620] 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
1615 cpg binding protein (protein containing phd finger and cxxc domain 1). [swissprot;acc:q9p0u4] 205.179 200.988

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/