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 1875 to 1924 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
469 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Subtracted Low confidence 7870.27 8267.28 397.01
ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] High confidence 11143.5 10276.3 867.2
470 block of proliferation 1. [swissprot;acc:q14137] Divided 3796.24 4348.59 1.1455
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Subtracted Low confidence 7870.27 8267.28 397.01
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] High confidence 5367.04 6233.12 866.08
probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] Divided Low confidence 7702.99 8088.26 1.05002
471 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] High confidence 9649.61 11053.5 1.14549
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Subtracted 5980.15 6843.48 863.33
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171] Low confidence 8683.9 9080.72 396.82
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Divided 7702.99 8088.26 1.05002
472 kinesin-associated protein 3 (smg gds-associated protein). [swissprot;acc:q92845]
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Subtracted High confidence 5246.01 6109.31 863.3
rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Low confidence 7155.19 7551.48 396.29
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided High confidence 9649.61 11053.5 1.14549
473 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Subtracted Low confidence 8686.89 9082.91 396.02
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Divided 8840.55 9282.64 1.05001
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Subtracted High confidence 5979.95 6842.78 862.83
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Divided 9649.61 11053.5 1.14549
474 aquaporin 5. [swissprot;acc:p55064] Low confidence 8840.55 9282.64 1.05001
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Subtracted High confidence 5979.94 6842.76 862.82
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Low confidence 7849.54 8245.26 395.72
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Divided High confidence 9649.61 11053.5 1.14549
475 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Subtracted 5979.93 6842.72 862.79
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Divided Low confidence 8840.53 9282.62 1.05001
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] High confidence 9649.61 11053.5 1.14549
oligophrenin 1. [swissprot;acc:o60890] Subtracted Low confidence 6428.7 6824.22 395.52
476 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Divided 8840.39 9282.37 1.05
calsyntenin-1 precursor. [swissprot;acc:o94985] Subtracted 8675.77 9070.62 394.85
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Divided High confidence 9649.61 11053.5 1.14549
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Subtracted 5067.02 5926.46 859.44
477 endoplasmin precursor (94 kda glucose-regulated protein) (grp94) (gp96 homolog) (tumor rejection antigen 1). [swissprot;acc:p14625] Low confidence 8675.77 9070.62 394.85
nitrogen fixation cluster-like. [refseq;acc:nm_014301] Divided High confidence 9649.61 11053.5 1.14549
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9] Low confidence 8444.05 8865.49 1.04991
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Subtracted High confidence 5067 5926.17 859.17
478 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Low confidence 8674.94 9069.59 394.65
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] High confidence 5066.99 5926.1 859.11
star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8] Divided 9649.61 11053.5 1.14549
uxt protein (ubiquitously expressed transcript protein) (hspc024). [swissprot;acc:q9ubk9] Low confidence 8444.05 8865.49 1.04991
479 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Subtracted 8451.27 8845.91 394.64
alanine aminotransferase 2; glutamic-pyruvate transaminase 2. [refseq;acc:nm_133443] Divided 8754.87 9190.49 1.04976
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Subtracted High confidence 7170.83 8029.64 858.81
star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502] Divided 9649.61 11053.5 1.14549
480 bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Low confidence 8459.92 8880.14 1.04967
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Subtracted 8674.85 9069.48 394.63
neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822] Divided High confidence 9649.61 11053.5 1.14549
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 5066.93 5925.38 858.45
481 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 5493.1 6350.19 857.09
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Divided Low confidence 7722.25 8104.32 1.04948
cholecystokinin type a receptor (cck-a receptor) (cck-ar). [swissprot;acc:p32238] Subtracted 8674.21 9068.68 394.47
mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635] Divided High confidence 9649.61 11053.5 1.14549

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/