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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1263 to 1312 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
632 delta3,5-delta2,4-dienoyl-coa isomerase, mitochondrial precursor (ec 5.3.3.-). [swissprot;acc:q13011] Subtracted 229.072 216.576 12.496
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Divided 214.254 202.166 1.05979
633 actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313] Subtracted 229.072 216.576 12.496
alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided 234.106 248.104 1.05979
634 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 226.523 213.786 1.05958
synapsin i (brain protein 4.1). [swissprot;acc:p17600] Subtracted 229.072 216.576 12.496
635 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] Divided 228.639 242.258 1.05957
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Subtracted 235.296 247.673 12.377
636 splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Divided 228.639 242.258 1.05957
vav proto-oncogene. [swissprot;acc:p15498] Subtracted 212.2 199.849 12.351
637 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Divided 228.639 242.258 1.05957
vav-3 protein. [swissprot;acc:q9ukw4] Subtracted 212.253 199.908 12.345
638 sorting nexin 17. [swissprot;acc:q15036] Divided 228.639 242.258 1.05957
vav-2 protein. [swissprot;acc:p52735] Subtracted 212.526 200.212 12.314
639 nucleoporin-like protein rip (hiv-1 rev-binding protein) (rev interacting protein) (rev/rex activation domain-binding protein). [swissprot;acc:p52594] Divided 217.67 230.596 1.05938
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Subtracted 222.554 234.847 12.293
640 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 12.265
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Divided 217.67 230.596 1.05938
641 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Subtracted 244.842 232.577 12.265
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] Divided 217.67 230.596 1.05938
642 intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Subtracted 228.944 216.745 12.199
643 hiv-1 rev binding protein-like; rev/rex activation domain binding protein-related. [refseq;acc:nm_006076] Divided 217.67 230.596 1.05938
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Subtracted 218.227 206.078 12.149
644 cgthba protein (-14 gene protein). [swissprot;acc:q12980] Divided 217.67 230.596 1.05938
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Subtracted 226.497 214.355 12.142
645 hiv tat specific factor 1; cofactor required for tat activation of hiv-1 transcription. [refseq;acc:nm_014500] Divided 217.67 230.596 1.05938
hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Subtracted 226.497 214.355 12.142
646 short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Divided 216.731 229.549 1.05914
single-minded homolog 1. [swissprot;acc:p81133] Subtracted 226.497 214.355 12.142
647 dynein light chain 2. [refseq;acc:nm_080677] Divided 216.731 229.549 1.05914
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Subtracted 214.257 202.125 12.132
648 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 202.132 12.125
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Divided 218.227 206.078 1.05895
649 eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 233.725 220.751 1.05877
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Subtracted 214.257 202.132 12.125
650 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 202.135 12.122
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Divided 228.986 216.276 1.05877
651 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 233.725 220.751
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Subtracted 214.256 202.139 12.117
652 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Divided 248.994 235.255 1.0584
653 dok-like protein. [refseq;acc:nm_024872] 216.504 204.622 1.05807
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Subtracted 214.256 202.139 12.117
654 docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Divided 216.504 204.622 1.05807
phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167] Subtracted 214.256 202.139 12.117
655 docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Divided 216.504 204.622 1.05807
gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] Subtracted 214.256 202.14 12.116
656 gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Divided 216.504 204.622 1.05807

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/