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 8091 to 8140 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2023 pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] Rooted 70.2058 72.1264 1.02736
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Measured 3560.24 3364.84 1.05807
2024 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 5976.81 6323.87
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] Rooted 70.2058 72.1264 1.02736
lim protein (similar to rat protein kinase c-binding enigma); enigma homolog. [refseq;acc:nm_006457] Squared 25973 28320.7 1.09039
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Ranked 215.553 213.663 1.00885
2025 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 189.987 191.668
arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] Rooted 59.3853 61.0095 1.02735
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] Measured 4813.13 5091.36 1.05781
ring finger protein 20. [refseq;acc:nm_019592] Squared 24533.9 26751 1.09037
2026 26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231] Rooted 62.2803 63.9816 1.02732
aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Measured 6766.45 7155.54 1.0575
ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771] Squared 24533.9 26751 1.09037
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Ranked 215.553 213.663 1.00885
2027 e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409] Squared 25972.4 28319.2 1.09036
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Rooted 61.1916 62.8616 1.02729
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Ranked 225.015 223.041 1.00885
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Measured 6218.34 6575.81 1.05749
2028 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] 10243.4 9686.82 1.05746
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Squared 24791.1 27031.1 1.09036
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Rooted 59.7668 58.1847 1.02719
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Ranked 215.553 213.663 1.00885
2029 cytoplasmic cysteine conjugate-beta lyase; glutamine-phenylpyruvate aminotransferase. [refseq;acc:nm_004059] 189.999 191.677 1.00883
paraspeckle protein 1. [refseq;acc:nm_018282] Measured 10241.3 9685.21 1.05742
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] Rooted 61.2194 62.8837 1.02719
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Squared 24791.1 27031.1 1.09036
2030 alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Ranked 189.999 191.677 1.00883
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7] Squared 24791.1 27031.1 1.09036
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Rooted 59.7668 58.1847 1.02719
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Measured 5060.82 5350.93 1.05732
2031 calcipressin 1 (down syndrome critical region protein 1) (myocyte- enriched calcineurin interacting protein 1) (mcip1) (adapt78). [swissprot;acc:p53805] Squared 24791.1 27031.2 1.09036
eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198] Measured 5060.82 5350.93 1.05732
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Rooted 59.7668 58.1847 1.02719
traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614] Ranked 218.466 216.562 1.00879
2032 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Rooted 61.2194 62.8837 1.02719
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Squared 25972.4 28319.2 1.09036
f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] Ranked 215.322 213.46 1.00872
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Measured 5060.82 5350.93 1.05732
2033 atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] Rooted 61.2194 62.8837 1.02719
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Measured 6101.12 6449.87 1.05716
f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Ranked 215.322 213.46 1.00872
mitochondrial ribosomal protein l24. [refseq;acc:nm_024540] Squared 25972.4 28319.2 1.09036
2034 65 kda yes-associated protein (yap65). [swissprot;acc:p46937]
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] Ranked 218.919 220.812 1.00865
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Rooted 59.7668 58.1847 1.02719
topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027] Measured 6920.71 7315.59 1.05706
2035 9 kda protein. [swissprot;acc:p13994] Squared 25972.4 28319.2 1.09036
acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067] Measured 6920.71 7315.59 1.05706
centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] Ranked 218.919 220.812 1.00865
coatomer alpha subunit (alpha-coat protein) (alpha-cop) (hepcop) (hep-cop) [contains: xenin (xenopsin-related peptide); proxenin]. [swissprot;acc:p53621] Rooted 82.7892 80.6004 1.02716

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/