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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3151 to 3200 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
1576 epsin 1; eh domain-binding mitotic phosphoprotein. [refseq;acc:nm_013333] Low confidence 191.484 187.529 1.02109
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] High confidence 222.585 218.982 1.01645
1577 ammecr1 protein. [refseq;acc:nm_015365]
stress-70 protein, mitochondrial precursor (75 kda glucose regulated protein) (grp 75) (peptide-binding protein 74) (pbp74) (mortalin) (mot). [swissprot;acc:p38646] Low confidence 201.171 197.018 1.02108
1578 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] High confidence 222.585 218.982 1.01645
ran gtpase-activating protein 1. [swissprot;acc:p46060] Low confidence 201.348 197.194 1.02107
1579 cda11 protein. [refseq;acc:nm_032026] High confidence 213.181 209.732 1.01644
metastasis-associated protein mta1. [swissprot;acc:q13330] Low confidence 200.699 196.56 1.02106
1580 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 208.899 213.298
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] High confidence 168.018 170.769 1.01637
1581 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 168.002 170.753
dnaj homolog subfamily a member 4. [swissprot;acc:q8ww22] Low confidence 196.957 192.894 1.02106
1582 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] High confidence 168.098 170.844 1.01634
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Low confidence 200.342 196.211 1.02105
1583 atp-binding cassette, sub-family d, member 2 (adrenoleukodystrophy related protein) (haldr) (adrenoleukodystrophy-like 1). [swissprot;acc:q9ubj2] 202.41 206.669 1.02104
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] High confidence 168.091 170.837 1.01634
1584 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] 216.891 220.432 1.01633
aflatoxin b1 aldehyde reductase 2 (ec 1.-.-.-) (afb1-ar 2). [swissprot;acc:o95154] Low confidence 190.926 186.991 1.02104
1585 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] High confidence 168.145 170.888 1.01631
fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306] Low confidence 202.247 198.08 1.02104
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] High confidence 222.166 225.79 1.01631
aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488] Low confidence 190.955 187.021 1.02104
1587 neuropeptide y receptor type 2 (npy2-r) (npy-y2 receptor). [swissprot;acc:p49146] 208.896 213.29 1.02103
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] High confidence 220.129 216.598 1.0163
1588 phd finger protein 9. [refseq;acc:nm_018062] Low confidence 204.272 200.064 1.02103
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] High confidence 177.834 180.725 1.01626
1589 spastin. [swissprot;acc:q9ubp0] Low confidence 201.306 197.159 1.02103
valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] High confidence 223.589 227.219 1.01624
1590 thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919] Low confidence 198.345 194.261 1.02102
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

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/