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 [...,...].
Value Type Interaction Map Gene green Rank Filtered description Network Comparison Type network_comparison red
Results: HTML CSV LaTeX Showing element 1730 to 1779 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Network Comparison Type  : Divided
green
Rank
description
network_comparison
red
213.875 1389 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 1.02148 218.47
1390 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]
1391 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
1393 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]
1394 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
213.876 1377 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] 218.471
1378 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] 218.47
1380 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]
1381 rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]
1382 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
1383 adaptor-associated kinase 1. [refseq;acc:nm_014911]
1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] 218.471
1386 rho-gtpase activating protein 10. [refseq;acc:nm_020824] 218.47
1388 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 218.471
1392 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]
1395 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 218.47
213.889 1678 serine/threonine protein kinase 23 (ec 2.7.1.37) (muscle-specific serine kinase 1) (mssk-1). [swissprot;acc:q9upe1] 1.01407 216.899
1679 gtp binding protein 2. [refseq;acc:nm_019096]
1680 cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]
1681 dna segment on chromosome 6(unique) 2654 expressed sequence; dna segment on chromosome x (unique) 2654 expressed sequence. [refseq;acc:nm_012135]
1682 sfrs protein kinase 2 isoform b. [refseq;acc:nm_182691]
1683 cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]
1684 sfrs protein kinase 1; sr protein kinase 1. [refseq;acc:nm_003137]
1685 xap-5 protein (hxc-26 protein). [swissprot;acc:q14320]
213.897 1614 hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261] 1.0156 217.233
213.899 1363 camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1.02194 218.591
213.91 1376 eyes absent homolog 3. [swissprot;acc:q99504] 1.02163 218.537
213.912 826 60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993] 1.04335 223.186
213.914 1602 phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] 1.01599 217.334
213.916 1605 hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] 1.01592 217.322
213.945 572 cbf1 interacting corepressor. [refseq;acc:nm_004882] 1.06504 227.86
573 evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025]
214.021 1528 hepatocyte nuclear factor 3-gamma (hnf-3g) (forkhead box protein a3) (fork head-related protein fkh h3). [swissprot;acc:p55318] 1.01759 217.785
214.041 1160 2-oxoglutarate dehydrogenase e1 component, mitochondrial precursor (ec 1.2.4.2) (alpha-ketoglutarate dehydrogenase). [swissprot;acc:q02218] 1.02633 208.55
214.049 1397 40s ribosomal protein s8. [swissprot;acc:p09058] 1.02145 218.64
214.11 1401 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 1.02124 218.657
214.118 1400 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 1.02125 218.667
214.148 2354 copper-transporting atpase 2 (ec 3.6.3.4) (copper pump 2) (wilson disease-associated protein). [swissprot;acc:p35670] 1.00434 215.078
214.149 1502 uridine kinase-like 1. [swissprot;acc:q9nwz5] 1.01838 218.084
1644 secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] 1.01451 217.256
1645 prefoldin subunit 1. [swissprot;acc:o60925]
1646 secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]
1647 choline dehydrogenase. [refseq;acc:nm_018397]
214.155 2352 copper-transporting atpase 1 (ec 3.6.3.4) (copper pump 1) (menkes disease-associated protein). [swissprot;acc:q04656] 1.00436 215.088
214.184 2604 cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 1.00141 214.486
214.19 2206 transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] 1.00645 215.571
214.192 2603 cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 1.00141 214.494
214.193 2605 tcd37 homolog; prune. [refseq;acc:nm_021222] 214.495
214.194 2232 43 kda receptor-associated protein of the synapse (rapsyn) (acetylcholine receptor-associated 43 kda protein) (43 kda postsynaptic protein). [swissprot;acc:q13702] 1.00632 215.547
214.198 2606 cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 1.00141 214.5

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/