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 Value Type Gene description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 2714 to 2763 of 12912 in total
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
Value Type
description
red
green
network_comparison
679 Ranked homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 132.413 125.389 1.05602
Squared dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658] 22337.3 26234.1 1.17445
Rooted putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] 61.5558 66.1861 1.07522
680 Measured adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] 6503.03 7282.5 1.11986
Ranked homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 132.413 125.389 1.05602
Squared seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [swissprot;acc:q12884] 22336.8 26233.5 1.17445
Rooted t54 protein. [swissprot;acc:q92917] 61.5558 66.1861 1.07522
681 Measured ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 7170.83 8029.64 1.11976
Ranked homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 132.413 125.389 1.05602
Squared cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [refseq;acc:nm_004376] 22335.8 26232.2 1.17445
Rooted oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 80.2562 86.277 1.07502
682 Measured syntaxin 12. [refseq;acc:nm_177424] 5552.92 6217.59 1.1197
Ranked homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 132.413 125.389 1.05602
Squared protoheme ix farnesyltransferase, mitochondrial precursor (ec 2.5.1.-) (heme o synthase). [swissprot;acc:q12887] 22335.8 26232.2 1.17445
Rooted stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] 86.5959 93.0684 1.07474
683 Measured sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 7139.5 7994.06 1.11969
Ranked homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 132.413 125.389 1.05602
Squared [pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [swissprot;acc:q15118] 22328.1 26222.3 1.17441
Rooted tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] 72.8809 78.3254 1.0747
684 Measured eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 4359.82 4880.99 1.11954
Ranked homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 132.413 125.389 1.05602
Squared [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] 22328.2 26222.4 1.17441
Rooted transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] 72.9862 78.4342 1.07464
685 Measured metaxin 1. [swissprot;acc:q13505] 9327.58 10442.2 1.1195
Ranked homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 132.413 125.389 1.05602
Squared translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] 42363.8 36083.8 1.17404
Rooted hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 57.4644 61.7491 1.07456
686 Measured 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] 6920.69 7747.63 1.11949
Ranked homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 132.413 125.389 1.05602
Squared peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] 28982.3 34012.8 1.17357
Rooted c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] 86.4264 92.8635 1.07448
687 Measured 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] 6920.71 7747.65 1.11949
Ranked retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 132.413 125.389 1.05602
Squared meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] 24633.6 28893.6 1.17293
Rooted putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] 57.6308 61.9165 1.07436
688 Measured 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 6920.67 7747.6 1.11949
Ranked dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 237.554 250.823 1.05586
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

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/