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 red Network Comparison Type Value Type green Rank Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 858 to 907 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
green
Rank
description
network_comparison
4355.61 5810.82 128 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1.3341
4358.13 5811.49 129 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1.33348
4359.82 4880.99 684 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 1.11954
4366.44 5899.76 108 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1.35116
109 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
110 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
111 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
112 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
4367.69 4438.77 2599 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 1.01627
4368.44 4539.34 2400 malate dehydrogenase, mitochondrial precursor (ec 1.1.1.37). [swissprot;acc:p40926] 1.03912
4374.32 4126.96 1963 phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 1.05994
1964 pp3111 protein. [refseq;acc:nm_022156]
1965 syntaxin 18. [swissprot;acc:q9p2w9]
1966 rd protein. [swissprot;acc:p18615]
1968 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]
1969 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
1970 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]
1971 j domain containing protein 1. [swissprot;acc:q9ukb3]
1972 sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]
1973 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
4379.28 4803.59 959 sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 1.09689
4383.34 4642.93 1989 m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305] 1.05922
4392.63 4776.19 1178 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 1.08732
1179 solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749]
1180 farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324]
1181 protocadherin 15 precursor. [swissprot;acc:q96qu1]
1182 solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415]
1183 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]
1184 zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151]
1185 suppressor of fused. [refseq;acc:nm_016169]
1186 zinc finger protein gli3. [swissprot;acc:p10071]
1187 limb region 1 protein; limb region 1. [refseq;acc:nm_022458]
1188 gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
1189 zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070]
4405.4 5782.08 141 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 1.3125
4413.55 4784.6 1249 trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 1.08407
4418.21 4594.87 2388 diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] 1.03998
4446.72 5553.79 212 transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 1.24896
213 nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
4450.17 4721.37 1940 m-phase inducer phosphatase 3 (ec 3.1.3.48) (dual specificity phosphatase cdc25c). [swissprot;acc:p30307] 1.06094
4450.84 4517.54 2606 tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 1.01499
4455.95 5774.03 174 mad protein (max dimerizer). [swissprot;acc:q05195] 1.2958
4456.67 5773.77 175 max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] 1.29553
4456.93 5773.67 176 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] 1.29544
4457.06 5773.63 177 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] 1.29539
4457.6 4642.72 2382 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] 1.04153
4483.08 4971.62 815 midasin (midas-containing protein). [swissprot;acc:q9nu22] 1.10897
4483.26 4917.77 957 structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] 1.09692
958 chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]

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/