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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Gene Network Comparison Type red Value Type green Rank Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 1018 to 1067 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
green
Rank
description
network_comparison
4757.46 5198.91 1044 mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517] 1.09279
1046 skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
1047 ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
1048 tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
1049 sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
1050 neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
1051 homeobox protein dlx-2. [swissprot;acc:q07687]
1052 homeobox protein dlx-5. [swissprot;acc:p56178]
1053 fetal brain protein 239 (239fb). [swissprot;acc:q15777]
1054 homeobox protein dlx-3. [swissprot;acc:o60479]
1055 activated p21cdc42hs kinase. [refseq;acc:nm_005781]
1056 mitogen-activated protein kinase kinase kinase 7 interacting protein 2 isoform 1; tak1-binding protein 2. [refseq;acc:nm_015093]
4763.99 4868.66 2546 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] 1.02197
4771.21 5961.43 207 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 1.24946
4775.11 5438.18 527 protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] 1.13886
4775.25 5158.86 1332 my016 protein. [sptrembl;acc:q9h3k6] 1.08033
4778.28 4732.13 2646 mct-1 protein. [refseq;acc:nm_014060] 1.00975
2647 mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
4783.49 5097.66 1806 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] 1.06568
4800.81 7132.71 78 cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 1.48573
4806.33 5066.92 2126 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 1.05422
4806.38 5067 2125 ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]
4808.79 6074.21 200 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 1.26315
4810.22 6075.04 201 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 1.26294
4810.71 5413.89 645 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] 1.12538
4810.85 5414.21 641 peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911] 1.12542
5414.22 644 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
5414.23 642 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]
643 polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]
4811.02 5414.64 640 glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712] 1.12547
4812.01 6076.09 202 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1.26269
4813.13 5091.36 2025 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1.05781
4824.49 4813.92 2743 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 1.0022
4835.55 5243.23 1244 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] 1.08431
1245 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
4846.16 5283.08 1108 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] 1.09016
4855.46 5824.52 304 pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] 1.19958
4857.03 5039.78 2418 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 1.03763
2419 thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
2420 thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]
4858.96 5568.85 464 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 1.1461
4860.34 5127.3 2102 c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586] 1.05493
4864.25 5573.62 467 metastasis-associated protein mta1. [swissprot;acc:q13330] 1.14583
4864.66 5514.87 602 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 1.13366
603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]
4869.15 5578.02 468 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 1.14558
4871.11 5129.63 2151 early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] 1.05307
4877.74 4890.64 2739 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 1.00264
4883.73 4982.88 2556 shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] 1.0203
4884.35 4985.78 2552 ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346] 1.02077

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/