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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Gene Rank Network Comparison Type description Value Type Filtered Interaction Map network_comparison red green
Results: HTML CSV LaTeX Showing element 76424 to 76473 of 77072 in total
Filtered  : 1
Interaction Map  : Low confidence
Rank
Network Comparison Type
description
Value Type
network_comparison
red
green
4980 Subtracted sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Measured 19.01 8650.11 8669.12
4981 Divided aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Rooted 1.00413 68.5409 68.8242
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Squared 1.002 41230.7 41148.6
kinesin-like protein kif3a (microtubule plus end-directed kinesin motor 3a). [swissprot;acc:q9y496] Ranked 1.00072 193.278 193.418
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Measured 1.00225 7681.66 7698.93
Subtracted guanine nucleotide-binding protein g(t), alpha-2 subunit (transducin alpha-2 chain). [swissprot;acc:p19087] Squared 82.8 41226.4 41143.6
kinesin-like protein kif3a (microtubule plus end-directed kinesin motor 3a). [swissprot;acc:q9y496] Ranked 0.14 193.278 193.418
nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818] Rooted 0.289 67.6444 67.9334
solute carrier family 35, member e2. [refseq;acc:nm_182838] Measured 17.56 7238.71 7256.27
4982 Divided cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 1.00224 7619.32 7636.37
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 1.00191 41254.3 41175.8
neuronal shc. [refseq;acc:nm_016848] Ranked 1.00066 205.038 205.174
pap-1 binding protein. [refseq;acc:nm_031288] Rooted 1.00403 66.3661 66.6337
Subtracted guanine nucleotide-binding protein g(t), alpha-1 subunit (transducin alpha-1 chain). [swissprot;acc:p11488] Squared 82.6 41227.8 41145.2
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 0.287 72.0846 71.7976
neuronal shc. [refseq;acc:nm_016848] Ranked 0.136 205.038 205.174
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Measured 17.27 7681.66 7698.93
4983 Divided guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Squared 1.0019 41256.7 41178.5
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted 1.00401 67.8798 68.1519
protein sck (fragment). [swissprot;acc:p98077] Ranked 1.00065 205.037 205.171
sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] Measured 1.0022 8650.11 8669.12
Subtracted aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Rooted 0.2833 68.5409 68.8242
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Measured 17.05 7619.32 7636.37
guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086] Squared 82.1 41230.7 41148.6
protein sck (fragment). [swissprot;acc:p98077] Ranked 0.134 205.037 205.171
4984 Divided cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Squared 1.0018 46813.3 46897.5
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 1.00063 202.785 202.913
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Rooted 1.004 72.0846 71.7976
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 1.0021 7525.15 7509.41
Subtracted cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Squared 79.9 46803.1 46883
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 0.128 202.785 202.913
fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Measured 17.02 8494.9 8511.92
intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Rooted 0.2829 84.6751 84.3922
4985 Divided cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Squared 1.00178 46810.8 46894.2
dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981] Rooted 1.0037 75.7327 76.0128
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Ranked 1.00058 198.253 198.368
fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413] Measured 1.002 8494.9 8511.92
Subtracted dual specificity protein kinase ttk (ec 2.7.1.-) (pyt). [swissprot;acc:p33981] Rooted 0.2801 75.7327 76.0128
fatty acid-binding protein, brain (b-fabp) (brain lipid-binding protein) (blbp) (mammary derived growth inhibitor related). [swissprot;acc:o15540] Ranked 0.115 198.253 198.368
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 78.5 41254.3 41175.8
sec13-related protein. [swissprot;acc:p55735] Measured 16.09 9039.42 9023.33
4986 Divided cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] Squared 1.00171 46803.1 46883
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Measured 1.00183 7527.87 7514.1
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Ranked 1.00052 198.568 198.464
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Rooted 1.00368 84.7958 84.4851
Subtracted fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Ranked 0.104 198.568 198.464
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Squared 78.2 41256.7 41178.5
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Rooted 0.2721 67.8798 68.1519
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Measured 15.74 7525.15 7509.41
4987 Divided intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811] Rooted 1.00335 84.6751 84.3922

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/