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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Filtered Value Type Gene network_comparison green Rank description Interaction Map red Network Comparison Type
Results: HTML CSV LaTeX Showing element 51 to 100 of 77072 in total
Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
network_comparison
green
Rank
description
Interaction Map
red
1.00153 1594.85 825 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Low confidence 1597.29
1.00157 1595.05 824 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 1597.55
1.00159 1595.12 823 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 1597.66
5046.33 492 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] High confidence 5038.33
822 Low confidence
1.00161 770.408 821 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 771.651
1.00182 1595.89 820 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 1598.8
1.00194 4459.15 819 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 4467.8
1.00223 22910.9 491 high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] High confidence 22962
1.00224 22888.8 490 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 22940.1
22895.1 489 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 22946.3
1.00225 249.857 487 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 250.419
488 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
1.00227 22826.8 486 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] 22878.7
1.00229 22797.8 485 high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 22850.1
1.00234 2071.52 818 actin, aortic smooth muscle (alpha-actin 2). [swissprot;acc:p03996] Low confidence 2076.36
1.00239 1148.47 817 timeless homolog. [refseq;acc:nm_003920] 1151.21
1.00256 1264.88 816 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 1268.12
1.00257 3822.12 815 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 3831.93
1.00267 6282.88 814 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 6266.18
1.00276 9860.07 813 uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] 9832.89
1.00278 961.098 484 scribble. [refseq;acc:nm_015356] High confidence 958.429
1.00289 1554.65 812 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] Low confidence 1550.17
1.0029 20672.6 483 probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] High confidence 20612.9
1.00296 6352.81 811 Low confidence 6334.04
1.00304 969.022 810 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 966.085
1.00317 1763.71 809 dna topoisomerase i (ec 5.99.1.2). [swissprot;acc:p11387] 1769.3
1.00326 7115.3 808 trinucleotide repeat containing 15. [refseq;acc:nm_015575] 7138.53
1.00339 1505.34 807 chorein (chorea-acanthocytosis protein). [swissprot;acc:q96rl7] 1510.44
1.00362 6099.89 806 high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] 6121.96
1.00367 6193.94 805 dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] 6216.67
1.00368 6179.55 804 high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 6202.32
1.00387 796.85 482 sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] High confidence 793.778
6330.06 803 nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Low confidence 6354.56
1.00398 6779.39 802 high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] 6806.37
1.00424 4703 801 butyrate-induced transcript 1. [refseq;acc:nm_016395] 4683.13
1.00442 1259.69 800 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 1254.15
1.00475 563.113 481 mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] High confidence 565.785
1475.19 799 spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Low confidence 1482.2
1.00479 1015.49 798 scratch; scratch 1. [refseq;acc:nm_031309] 1020.35
1.00488 6396.8 480 orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466] High confidence 6428
1.00489 1597.32 797 rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Low confidence 1605.13
1.0051 1775.53 796 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 1784.58
1.00535 2438.24 795 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 2425.26
1.00552 971.37 794 dystrophin. [swissprot;acc:p11532] 976.734
1.00557 9023.75 793 methyltransferase like 2. [refseq;acc:nm_018396] 8973.73
1.00558 1006.57 792 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 1012.19
1.00587 1310.67 479 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] High confidence 1318.37
1.00669 701.071 478 survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637] 705.758
1.00704 429 477 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 426

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.
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