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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2751 to 2800 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
688 Squared adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] 22245.5 26087.5 1.17271
Rooted dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 60.7997 65.3199 1.07435
689 Measured 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 6920.69 7747.63 1.11949
Ranked t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] 135.379 128.225 1.05579
Squared dendritic cell protein. [refseq;acc:nm_006360] 33104 38818.5 1.17262
Rooted hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] 100.684 108.135 1.074
690 Measured 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] 6920.69 7747.63 1.11949
Ranked nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 220.593 208.987 1.05553
Squared potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 33104 38818.5 1.17262
Rooted tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] 86.1101 92.4812 1.07399
691 Measured 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 6920.69 7747.63 1.11949
Ranked breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 217.602 206.195 1.05532
Squared carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 33104 38818.5 1.17262
Rooted potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 63.1365 67.8053 1.07395
692 Measured 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] 6920.69 7747.63 1.11949
Ranked cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] 217.602 206.195 1.05532
Squared cpz gene product. [refseq;acc:nm_003652] 33104 38818.5 1.17262
Rooted eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] 51.3598 55.1508 1.07381
693 Measured j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 7725.1 8647.74 1.11943
Ranked rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] 222.554 234.847 1.05524
Squared carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 33104 38818.5 1.17262
Rooted eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] 51.3598 55.1508 1.07381
694 Measured human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 7725.1 8647.74 1.11943
Ranked dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 241.907 229.35 1.05475
Squared potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 33104 38818.5 1.17262
Rooted pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 68.4526 73.4852 1.07352
695 Measured zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] 7725.1 8647.74 1.11943
Ranked peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] 226.135 214.405 1.05471
Squared sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] 22778.5 26693.1 1.17186
Rooted potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] 63.17 67.8116 1.07348
696 Measured human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 7725.1 8647.74 1.11943
Ranked sr rich protein. [refseq;acc:nm_032870] 225.293 213.64 1.05455
Squared 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] 22778.5 26693.1 1.17186
Rooted pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 68.433 73.4502 1.07332
697 Measured sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 7105.27 7953.71 1.11941
Ranked ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419
Squared ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] 22778.5 26693.1 1.17186
Rooted potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 63.1944 67.8162 1.07314
698 Measured armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 7101.95 7949.85 1.11939
Ranked mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] 220.437 209.118 1.05413
Squared red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] 17850.2 20913.9 1.17163
Rooted cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 128.909 120.173 1.0727
699 Measured histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 7101.94 7949.84 1.11939
Ranked cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] 220.438 209.118 1.05413
Squared histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 18148.6 21253.1 1.17106
Rooted ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 57.0263 61.1552 1.0724
700 Measured 40s ribosomal protein s28. [swissprot;acc:p25112] 7161.14 8015.92 1.11936
Ranked dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 220.438 209.118 1.05413
Squared u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 19072.5 22327.5 1.17066
Rooted ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] 57.0263 61.1552 1.0724

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/