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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4608 to 4657 of 7460 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1802 thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [swissprot;acc:p04818] Divided 4980.54 5307.81 1.06571
1803 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]
my016 protein. [sptrembl;acc:q9h3k6] Subtracted 4775.25 5158.86 383.61
1804 pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] 4392.63 4776.19 383.56
stromal cell-derived factor 2 precursor (sdf-2). [swissprot;acc:q99470] Divided 4980.54 5307.81 1.06571
1805 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] Subtracted 4392.63 4776.19 383.56
stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [swissprot;acc:q9hcn8] Divided 4980.54 5307.81 1.06571
1806 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] Subtracted 4392.63 4776.19 383.56
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Divided 4783.49 5097.66 1.06568
1807 endothelial-derived gene 1. [refseq;acc:nm_025205] 6399.54 6818.17 1.06542
protocadherin 15 precursor. [swissprot;acc:q96qu1] Subtracted 4392.63 4776.19 383.56
1808 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Divided 4941.92 5265.09 1.06539
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Subtracted 4392.63 4776.19 383.56
1809 epsin 3. [refseq;acc:nm_017957] Divided 5816.12 6196.21 1.06535
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Subtracted 4392.63 4776.19 383.56
1810 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Divided 6520.83 6946.75 1.06532
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Subtracted 4392.63 4776.19 383.56
1811 suppressor of fused. [refseq;acc:nm_016169]
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Divided 7659.42 8156.79 1.06494
1812 hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431] 5514.19 5871.64 1.06482
zinc finger protein gli3. [swissprot;acc:p10071] Subtracted 4392.63 4776.19 383.56
1813 dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Divided 5866.19 6245.4 1.06464
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Subtracted 4392.63 4776.19 383.56
1814 gastricsin precursor (ec 3.4.23.3) (pepsinogen c). [swissprot;acc:p20142]
heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238] Divided 5733.71 6104.26 1.06463
1815 junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624] 6104.77 6498.84 1.06455
zinc finger protein gli2 (tax helper protein). [swissprot;acc:p10070] Subtracted 4392.63 4776.19 383.56
1816 dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] 6555.42 6938.82 383.4
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122] Divided 5633.44 5997 1.06454
1817 lactoylglutathione lyase (ec 4.4.1.5) (methylglyoxalase) (aldoketomutase) (glyoxalase i) (glx i) (ketone-aldehyde mutase) (s-d-lactoylglutathione methylglyoxal lyase). [swissprot;acc:q04760] Subtracted 6555.42 6938.82 383.4
solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [swissprot;acc:q9uhi7] Divided 5633.44 5997 1.06454
1818 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]
lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330] Subtracted 6555.42 6938.82 383.4
1819 adp-ribosylation factor 4. [swissprot;acc:p18085] Divided 5633.44 5997 1.06454
mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039] Subtracted 6555.42 6938.82 383.4
1820 fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Divided 5633.44 5997 1.06454
lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260] Subtracted 6555.42 6938.82 383.4
1821 regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] 5683.17 6065.55 382.38
shc transforming protein. [swissprot;acc:p29353] Divided 5633.44 5997 1.06454
1822 thioredoxin interacting protein; upregulated by 1,25-dihydroxyvitamin d-3. [refseq;acc:nm_006472] Subtracted 5693.88 6075.25 381.37
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Divided 5633.44 5997 1.06454
1823 epsin 3. [refseq;acc:nm_017957] Subtracted 5816.12 6196.21 380.09
neuronal shc. [refseq;acc:nm_016848] Divided 5633.44 5997 1.06454
1824 adp-ribosylation factor 1. [swissprot;acc:p32889]
dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985] Subtracted 5866.19 6245.4 379.21
1825 heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Divided 5633.44 5997 1.06454
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Subtracted 6916.14 7295.24 379.1
1826 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]
adp-ribosylation factor 3. [swissprot;acc:p16587] Divided 5633.44 5997 1.06454
1827 protein sck (fragment). [swissprot;acc:p98077]

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/