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 8486 to 8535 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
2122 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Ranked 206.473 207.911 1.00696
kinesin light chain 1 (klc 1). [swissprot;acc:q07866] Rooted 62.6682 64.2106 1.02461
serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965] Squared 27436.1 29835.5 1.08745
2123 adp-ribosylation factor 4. [swissprot;acc:p18085] Ranked 221.248 222.788 1.00696
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Measured 5977.03 6301.76 1.05433
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] Squared 27436.1 29835.5 1.08745
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Rooted 62.668 64.2104 1.02461
2124 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70]
fused toes homolog; likely ortholog of mouse fused toes. [refseq;acc:nm_022476] Ranked 221.248 222.788 1.00696
lamin b1. [swissprot;acc:p20700] Measured 5977.09 6301.79 1.05432
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Squared 23392.8 25437 1.08739
2125 complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Rooted 64.8027 66.3961 1.02459
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Measured 4806.38 5067 1.05422
scribble. [refseq;acc:nm_015356] Squared 24695.4 26851.1 1.08729
shc transforming protein. [swissprot;acc:p29353] Ranked 221.248 222.788 1.00696
2126 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Measured 4806.33 5066.92 1.05422
sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238] Rooted 64.8027 66.3961 1.02459
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Squared 12189 13252.8 1.08728
zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [refseq;acc:nm_032389] Ranked 221.248 222.788 1.00696
2127 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Squared 12189 13252.8 1.08728
dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1] Rooted 60.0193 61.4716 1.0242
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Measured 5328.73 5616.59 1.05402
neuronal shc. [refseq;acc:nm_016848] Ranked 221.248 222.788 1.00696
2128 40s ribosomal protein s29. [swissprot;acc:p30054] Squared 12106.4 13163.1 1.08728
adp-ribosylation factor 1. [swissprot;acc:p32889] Ranked 221.248 222.788 1.00696
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Measured 5328.73 5616.59 1.05402
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Rooted 62.1891 60.7203 1.02419
2129 26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460] 62.0038 63.5033 1.02418
bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Measured 5328.73 5616.59 1.05402
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651] Ranked 221.248 222.788 1.00696
lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] Squared 24697 26852.3 1.08727
2130 adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186] Rooted 62.0038 63.5033 1.02418
adp-ribosylation factor 3. [swissprot;acc:p16587] Ranked 221.248 222.788 1.00696
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Measured 5328.73 5616.59 1.05402
proteasome subunit beta type 7 precursor (ec 3.4.25.1) (proteasome subunit z) (macropain chain z) (multicatalytic endopeptidase complex chain z). [swissprot;acc:q99436] Squared 26864 29206 1.08718
2131 f-actin capping protein alpha-3 subunit (capz alpha-3) (germ cell- specific protein 3). [swissprot;acc:q96kx2] 30593.4 33250.7 1.08686
gtp cyclohydrolase i (ec 3.5.4.16) (gtp-ch-i). [swissprot;acc:p30793] Ranked 226.277 227.851 1.00696
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Measured 5328.73 5616.59 1.05402
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] Rooted 62.0038 63.5033 1.02418
2132 f-actin capping protein beta subunit (capz beta). [swissprot;acc:p47756] Squared 30593.4 33250.7 1.08686
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Measured 5328.73 5616.59 1.05402
protein sck (fragment). [swissprot;acc:p98077] Ranked 221.248 222.788 1.00696
rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763] Rooted 62.0038 63.5033 1.02418
2133 eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Measured 5328.73 5616.59 1.05402
n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] Rooted 62.1887 60.7211 1.02417
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [swissprot;acc:p22736] Ranked 207.74 206.305 1.00696
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Squared 31589.1 34332.1 1.08683
2134 heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626] Ranked 221.248 222.788 1.00696
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] Rooted 62.1887 60.7211 1.02417
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] Squared 31589.1 34332.1 1.08683

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/