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 Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3630 to 3679 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1815 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]
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Subtracted 6916.14 7295.24 379.1
1828 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Divided 5633.44 5997 1.06454
hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507] Subtracted 6916.14 7295.24 379.1
1829 hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] Divided 5633.44 5997 1.06454
1830 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Subtracted 6916.14 7295.24 379.1
1831 homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]
solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [swissprot;acc:q9ugh3] Divided 5633.44 5997 1.06454
1832 dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [swissprot;acc:o14733]
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Subtracted 6916.14 7295.24 379.1
1833 5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914] Divided 6175.23 6572.85 1.06439
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Subtracted 6916.14 7295.24 379.1
1834 60s ribosomal protein l11. [swissprot;acc:p39026] Divided 3593.24 3375.93 1.06437
cofilin, non-muscle isoform (18 kda phosphoprotein) (p18). [swissprot;acc:p23528] Subtracted 6230.21 6608.64 378.43
1835 cofilin, muscle isoform (cofilin 2). [swissprot;acc:q9y281]
transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [swissprot;acc:q15560] Divided 5019.3 5342.36 1.06436
1836 destrin (actin-depolymerizing factor) (adf). [swissprot;acc:p18282] Subtracted 6230.21 6608.64 378.43
transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193] Divided 5019.3 5342.36 1.06436
1837 rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873] 5739.49 6108.72 1.06433
ubiquitin fusion degradation protein 1 homolog (ub fusion protein 1). [swissprot;acc:q92890] Subtracted 6230.21 6608.64 378.43
1838 atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956] Divided 5739.49 6108.72 1.06433
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Subtracted 6951.29 7329 377.71
1839 atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010] Divided 5739.49 6108.72 1.06433
serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Subtracted 6167.29 6544.12 376.83
1840 asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776] 6847.82 7223.51 375.69

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/