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 5158 to 5207 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2579 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Subtracted 6380.6 6476.18 95.58
2580 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Divided 4331.39 4252.8 1.01848
stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] Subtracted 6380.61 6476.19 95.58
2581 dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Divided 4570.81 4654.97 1.01841
serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] Subtracted 6380.61 6476.19 95.58
2582 dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Divided 3899.28 3829.53 1.01821
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Subtracted 6380.84 6476.41 95.57
2583 hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541] 3436.65 3531.96 95.31
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] Divided 3926.4 3857.88 1.01776
2584 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 4180.32 4253.46 1.0175
growth arrest and dna-damage-inducible protein gadd45 gamma (cytokine responsive protein cr6). [swissprot;acc:o95257] Subtracted 3436.65 3531.96 95.31
2585 growth arrest and dna-damage-inducible protein gadd45 alpha (dna- damage inducible transcript 1) (ddit1). [swissprot;acc:p24522]
rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480] Divided 4180.32 4253.46 1.0175
2586 hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235] Subtracted 3436.65 3531.96 95.31
map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Divided 4180.32 4253.46 1.0175
2587 growth arrest and dna-damage-inducible protein gadd45 beta (negative growth-regulatory protein myd118) (myeloid differentiation primary response protein myd118). [swissprot;acc:o75293] Subtracted 3436.65 3531.96 95.31
map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Divided 4180.32 4253.46 1.0175
2588 hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410] Subtracted 7197.82 7291.66 93.84
meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Divided 4180.32 4253.46 1.0175
2589 apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] 7181.3 7057.99 1.01747
dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Subtracted 3803.04 3710.01 93.03
2590 chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973] Divided 7551.88 7422.68 1.01741
translin. [swissprot;acc:q15631] Subtracted 4979.44 5071.53 92.09
2591 chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Divided 7550.12 7422.01 1.01726
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted 4979.44 5071.53 92.09
2592 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Divided 7169.01 7047.98 1.01717
2593 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Subtracted 3880.5 3788.42 92.08
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Divided 4921.84 5005.06 1.01691
2594 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]
ubiquilin 1 isoform 1. [refseq;acc:nm_013438] Subtracted 9125.08 9217 91.92
2595 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Divided 4921.84 5005.06 1.01691
insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47] Subtracted 7433.72 7525.14 91.42
2596 ba207c16.2 (fragment). [sptrembl;acc:q9nql7] 7017.82 7108.89 91.07
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Divided 4921.84 5005.06 1.01691
2597 ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131] Subtracted 9128.19 9218.44 90.25
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] Divided 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
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Subtracted 3847.84 3759.28 88.56
2599 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Divided 4367.69 4438.77 1.01627
ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985] Subtracted 3805.17 3718.86 86.31
2600 dihydrolipoamide dehydrogenase, mitochondrial precursor (ec 1.8.1.4) (glycine cleavage system l protein). [swissprot;acc:p09622] Divided 6185 6283.8 1.01597
dna-directed rna polymerase ii 19 kda polypeptide (ec 2.7.7.6) (rpb7). [swissprot;acc:p52433] Subtracted 4570.81 4654.97 84.16
2601 beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457] 9150.44 9234.09 83.65
rad50 homolog isoform 1. [refseq;acc:nm_005732] Divided 7222.12 7110.74 1.01566
2602 26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210] Subtracted 9150.44 9234.09 83.65
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Divided 7571.73 7688.39 1.01541
2603 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Subtracted 4921.84 5005.06 83.22
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Divided 7572.69 7689.04 1.01536
2604 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Subtracted 4921.84 5005.06 83.22

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/