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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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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3151 to 3200 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1576 AHCY adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Subtracted 215.389 211.833 3.556
NUP98 nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948] Divided 222.585 218.982 1.01645
1577 AMMECR1 ammecr1 protein. [refseq;acc:nm_015365]
PGLS 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Subtracted 216.891 220.432 3.541
1578 ATP5C1 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] 218.277 214.739 3.538
RAE1 mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406] Divided 222.585 218.982 1.01645
1579 ATP5O atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Subtracted 218.277 214.739 3.538
TATDN1 cda11 protein. [refseq;acc:nm_032026] Divided 213.181 209.732 1.01644
1580 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 168.018 170.769 1.01637
R3HDM1 r3h domain protein 1. [swissprot;acc:q15032] Subtracted 218.105 214.573 3.532
1581 C20orf4 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 220.129 216.598 3.531
CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Divided 168.002 170.753 1.01637
1582 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 168.098 170.844 1.01634
TCEA2 transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Subtracted 227.768 231.246 3.478
1583 no value transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]
CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Divided 168.091 170.837 1.01634
1584 no value enthoprotin; epsin 4; clathrin interacting protein localized in the trans-golgi region. [refseq;acc:nm_014666] Subtracted 221.426 224.902 3.476
PGLS 6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336] Divided 216.891 220.432 1.01633
1585 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 168.145 170.888 1.01631
DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Subtracted 217.871 214.404 3.467
1586 AP1B1 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] Divided 222.166 225.79 1.01631
PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Subtracted 230.643 227.194 3.449
1587 C20orf4 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Divided 220.129 216.598 1.0163
TATDN1 cda11 protein. [refseq;acc:nm_032026] Subtracted 213.181 209.732 3.449
1588 KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 181.882 178.438 3.444
RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Divided 177.834 180.725 1.01626
1589 CEP70 p10-binding protein. [refseq;acc:nm_024491] Subtracted 221.313 217.877 3.436
VARS valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [swissprot;acc:p26640] Divided 223.589 227.219 1.01624
1590 NAGS n-acetylglutamate synthase. [refseq;acc:nm_153006] Subtracted 223.179 226.611 3.432
TYMS thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Divided 225.119 228.769 1.01621
1591 no value dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
PMM2 phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Subtracted 217.268 213.842 3.426
1592 GTF2B transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] 228.611 225.185
SDF2 stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Divided 225.119 228.769 1.01621
1593 SDF2L1 stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8]
ZNHIT3 thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Subtracted 228.611 225.185 3.426
1594 JPH4 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
NHP2L1 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 no value 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
NUFIP1 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 AP1G1 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
PMM1 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Subtracted 217.334 213.914 3.42
1597 AP1S3 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
FOXA1 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] Subtracted 217.322 213.916 3.406
1598 no value heat shock factor binding protein 1. [swissprot;acc:o75506] 216.62 213.22 3.4
AP1S1 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
1599 CLK2 protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Subtracted 214.984 211.614 3.37
DTNBP1 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Divided 217.871 214.404 1.01617
1600 AP2B1 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] 222.103 225.675 1.01608
CLK3 protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761] Subtracted 214.982 211.622 3.36

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
- Hugo is the HGNC identifier if it exists
- 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/