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 3758 to 3807 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1879 nucleoporin like 1. [refseq;acc:nm_014089] Subtracted 6174.74 6538.73 363.99
1880 d(4) dopamine receptor (d(2c) dopamine receptor). [swissprot;acc:p21917] Divided 6076.66 6463.12 1.0636
rho guanine nucleotide exchange factor 4 isoform a; apc-stimulated guanine nucleotide exchange factor. [refseq;acc:nm_015320] Subtracted 6174.74 6538.73 363.99
1881 cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Divided 6076.68 6462.56 1.0635
1882 eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [swissprot;acc:p20042] Subtracted 5423.67 5787.46 363.79
eukaryotic translation initiation factor 2 subunit 3 (eukaryotic translation initiation factor 2 gamma subunit) (eif-2-gamma). [swissprot;acc:p41091] Divided 5490.24 5838.67 1.06346
1883 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 5826 6195.48 1.06342
transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3] Subtracted 5949.31 6313.1 363.79
1884 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Divided 5826 6195.48 1.06342
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] Subtracted 5633.44 5997 363.56
1885 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]
ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5] Divided 5826 6195.48 1.06342
1886 heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991] Subtracted 5633.44 5997 363.56
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Divided 5826 6195.48 1.06342
1887 adp-ribosylation factor 4. [swissprot;acc:p18085] Subtracted 5633.44 5997 363.56
protein regulator of cytokinesis 1; protein regulating cytokinesis 1. [refseq;acc:nm_003981] Divided 5438.6 5783.11 1.06335
1888 bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Subtracted 5633.44 5997 363.56
1889 shc transforming protein. [swissprot;acc:p29353]
testis-specific bromodomain protein. [refseq;acc:nm_001726] Divided 5438.68 5783.2 1.06335
1890 nag14 protein. [refseq;acc:nm_022143] 5438.6 5783.11
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Subtracted 5633.44 5997 363.56
1891 bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059] Divided 5438.18 5782.62 1.06334
neuronal shc. [refseq;acc:nm_016848] Subtracted 5633.44 5997 363.56
1892 adp-ribosylation factor 1. [swissprot;acc:p32889]
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440] Divided 5438.52 5783.01 1.06334
1893 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 6830.4 7261.98 1.06319
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Subtracted 5633.44 5997 363.56
1894 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 3598.08 3384.59 1.06308
adp-ribosylation factor 3. [swissprot;acc:p16587] Subtracted 5633.44 5997 363.56
1895 protein sck (fragment). [swissprot;acc:p98077]
ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265] Divided 5882.1 6252.66 1.063
1896 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Subtracted 5633.44 5997 363.56
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Divided 4521 4805.16 1.06285
1897 ovarian carcinoma immunoreactive antigen. [refseq;acc:nm_017830] Subtracted 5633.44 5997 363.56
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Divided 4590.74 4879.11 1.06282
1898 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 6885.11 7317.48 1.0628
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Subtracted 5633.44 5997 363.56
1899 ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Divided 5786.36 6149.1 1.06269
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] Subtracted 5633.44 5997 363.56
1900 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]
seven in absentia homolog 2. [refseq;acc:nm_005067] Divided 5399.47 5737.79 1.06266
1901 inorganic pyrophosphatase (ec 3.6.1.1) (pyrophosphate phospho- hydrolase) (ppase). [swissprot;acc:q15181] 5204.25 5530.11 1.06261
ruvb-like 2 (ec 3.6.1.-) (48-kda tata box-binding protein-interacting protein) (48-kda tbp-interacting protein) (tip49b) (repressing pontin 52) (reptin 52) (51 kda erythrocyte cytosolic protein) (ecp-51) (tip60-associated protein 54-beta) (tap54-beta) (cgi-46). [swissprot;acc:q9y230] Subtracted 5786.36 6149.1 362.74
1902 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] 6884.69 7247.36 362.67
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Divided 5204.25 5530.11 1.06261
1903 aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9]
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Subtracted 6952.66 7315.06 362.4
1904 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Divided 5204.25 5530.11 1.06261

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/