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 12364 to 12413 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2589 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Squared 20043.6 20854.9 1.04048
2590 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Rooted 62.9549 63.4703 1.00819
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] Measured 7551.88 7422.68 1.01741
proteasome subunit alpha type 6 (ec 3.4.25.1) (proteasome iota chain) (macropain iota chain) (multicatalytic endopeptidase complex iota chain) (27 kda prosomal protein) (pros-27) (p27k). [swissprot;acc:p34062] Ranked 214.605 214.287 1.00148
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] Squared 11520.8 11074.7 1.04028
2591 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Rooted 62.955 63.4703 1.00819
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Measured 7550.12 7422.01 1.01726
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Squared 15965.2 15351.1 1.04
polybromo 1. [refseq;acc:nm_018165] Ranked 220.02 219.696 1.00147
2592 sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Rooted 62.9549 63.4703 1.00819
swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601] Ranked 220.02 219.696 1.00147
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Measured 7169.01 7047.98 1.01717
ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] Squared 36088.6 34704 1.0399
2593 adiponectin receptor 2. [refseq;acc:nm_024551] 13573.9 14111.2 1.03958
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Measured 4921.84 5005.06 1.01691
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532] Ranked 220.02 219.696 1.00147
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Rooted 62.9549 63.4703 1.00819
2594 conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7] Squared 37823.8 36386.7 1.0395
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] Rooted 56.0026 55.5558 1.00804
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Measured 4921.84 5005.06 1.01691
possible global transcription activator snf2l1. [swissprot;acc:p28370] Ranked 220.02 219.696 1.00147
2595 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Rooted 56.0046 55.5599 1.008
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Measured 4921.84 5005.06 1.01691
rad50 homolog isoform 1. [refseq;acc:nm_005732] Squared 33669.7 32433.8 1.03811
tbp-associated factor 172 (taf-172) (taf(ii)170). [swissprot;acc:o14981] Ranked 220.02 219.696 1.00147
2596 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Rooted 62.375 62.8643 1.00784
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Measured 4921.84 5005.06 1.01691
mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] Squared 36515.3 37901.1 1.03795
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531] Ranked 220.02 219.696 1.00147
2597 mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] Squared 36515.3 37901.1 1.03795
phd finger protein 9. [refseq;acc:nm_018062] Rooted 62.375 62.8643 1.00784
ran binding protein 11. [refseq;acc:nm_016338] Ranked 212.711 212.401 1.00146
ubiquitin-conjugating enzyme e2-17 kda 2 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 2). [swissprot;acc:p51669] Measured 8104.84 7970.2 1.01689
2598 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 7538.48 7417.58 1.0163
cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833] Squared 36515.3 37901.1 1.03795
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Rooted 62.375 62.8643 1.00784
transcription initiation factor tfiid 100 kda subunit (tafii-100) (tafii100). [swissprot;acc:q15542] Ranked 202.142 202.436 1.00145
2599 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Measured 4367.69 4438.77 1.01627
ba207c16.2 (fragment). [sptrembl;acc:q9nql7] Ranked 211.662 211.361 1.00142
mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Squared 36515.3 37901.1 1.03795
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Rooted 67.3258 66.8099 1.00772
2600 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Measured 6185 6283.8 1.01597
histone deacetylase 11 (hd11). [swissprot;acc:q96db2] Squared 36515.3 37901.1 1.03795
interferon-related developmental regulator 2 (skmc15 protein). [swissprot;acc:q12894] Ranked 224.877 225.193 1.00141
tripartite motif protein 2. [swissprot;acc:q9c040] Rooted 71.1211 71.6671 1.00768
2601 cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] Ranked 214.502 214.2 1.00141
ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Squared 36515.3 37901.1 1.03795
glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1. [refseq;acc:nm_018292] Rooted 63.7406 64.2205 1.00753
rad50 homolog isoform 1. [refseq;acc:nm_005732] Measured 7222.12 7110.74 1.01566
2602 arp2/3 complex 16 kda subunit (p16-arc) (actin-related protein 2/3 complex subunit 5). [swissprot;acc:o15511] Ranked 224.875 225.192 1.00141

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/