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 977 to 1026 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted High confidence 0 12335.3 10506.8 1828.5
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Low confidence 9271.76 11128.5 1856.74
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided High confidence 1 269.23 327.601 1.21681
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Low confidence 0 11725.7 13865.5 1.18249
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 1 202.96 190.094 1.06768
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted High confidence 227.032 193.056 33.976
striatin. [swissprot;acc:o43815] Low confidence 214.085 200.796 13.289
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided High confidence 0 11522.8 13684.9 1.18764
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 12328.5 10501 1827.5
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] Low confidence 1 220.268 206.997 13.271
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] Divided High confidence 208.52 171.595 1.21519
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted Low confidence 0 18241.7 16405 1836.7
natural resistance-associated macrophage protein 2 (nramp 2) (divalent metal transporter 1) (dmt1). [swissprot;acc:p49281] Divided 1 224.763 210.566 1.06742
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted High confidence 285.684 252.234 33.45
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] Divided Low confidence 0 9351.39 11039.5 1.18052
zinc finger imprinted 2. [swissprot;acc:q9nzv7] High confidence 11520.7 13680.4 1.18746
125 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Low confidence 1 213.243 227.616 1.0674
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted High confidence 0 12314.9 10489.3 1825.6
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1 208.588 171.778 1.21429
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 22038 18578 1.18624
prominin-like protein 1 precursor (antigen ac133) (cd133 antigen). [swissprot;acc:o43490] Subtracted Low confidence 1 220.268 206.997 13.271
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] High confidence 285.684 252.234 33.45
small edrk-rich factor 1a. [swissprot;acc:o75920] Divided Low confidence 0 4824.5 5690.5 1.1795
tpte and pten homologous inositol lipid phosphatase. [refseq;acc:nm_130785] Subtracted 15948.5 14125.4 1823.1
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided High confidence 1 94 114 1.21277
bromodomain adjacent to zinc finger domain protein 1a (atp-utilizing chromatin assembly and remodeling factor 1) (hacf1) (atp-dependent chromatin remodelling protein) (williams syndrome transcription factor-related chromatin remodeling factor 180) (wcrf180) (hwalp1) (chrac subunit acf1) (hspc317). [swissprot;acc:q9nrl2] Low confidence 0 14899.4 17562.2 1.17872
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Subtracted High confidence 12314.9 10489.3 1825.6
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 1 285.684 252.234 33.45
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Divided Low confidence 191.688 179.639 1.06707
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 226.892 213.661 13.231
putative protein-tyrosine phosphatase tpte (ec 3.1.3.48). [swissprot;acc:p56180] 0 15945.5 14123.3 1822.2
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Divided High confidence 9722.71 11493.8 1.18216
127 adenomatous polyposis coli protein (apc protein). [swissprot;acc:p25054] Subtracted Low confidence 1 222.31 235.538 13.228
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] High confidence 0 11732 13530.6 1798.6
cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 285.684 252.234 33.45
dna helicase homolog (fragment). [sptrembl;acc:q9y645] Low confidence 0 16660.8 18475.5 1814.7
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Divided High confidence 1 94 114 1.21277
scribble. [refseq;acc:nm_015356] Low confidence 0 10041.1 11814.4 1.1766
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] High confidence 9411.34 11119.7 1.18152
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Low confidence 1 203.678 190.88 1.06705
128 60s ribosomal protein l39. [swissprot;acc:p02404] High confidence 0 11564.4 9794.29 1.18073
adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted Low confidence 1 222.34 235.547 13.207
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided High confidence 94 114 1.21277
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8] Low confidence 0 9259.51 10879.6 1.17496
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 11161.3 12965.5 1804.2
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] High confidence 1 285.684 252.234 33.45
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 0 9722.71 11493.8 1771.09
striatin. [swissprot;acc:o43815] Divided Low confidence 1 214.085 200.796 1.06618
129 60s ribosomal protein l39. [swissprot;acc:p02404] Subtracted High confidence 0 11564.4 9794.29 1770.11
cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 285.684 252.234 33.45

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/