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 1673 to 1722 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
105 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] Ranked Divided 1 266.716 333.165 1.24914
musashi 1. [refseq;acc:nm_002442] Measured 4241.57 5810.79 1.36996
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Subtracted 11068 8508.5 2559.5
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Squared 90432.9 56304.2 34128.7
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Rooted 63.7477 48.1588 15.5889
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Ranked 0 11853.5 9808.86 2044.64
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Rooted 13.0525 17.6565 4.604
transcription factor jun-d. [swissprot;acc:p17535] Ranked 1 200.941 158.941 42
106 brain protein 16. [refseq;acc:nm_016458] 0 6890.54 4854.99 2035.55
casein kinase i alpha s-like. [refseq;acc:nm_145203] Squared 7795.92 9052.52 1256.6
cytohesin 4. [swissprot;acc:q9uia0] Divided 1 407289 263351 1.54656
elongation factor ts, mitochondrial precursor (ef-ts) (ef-tsmt). [swissprot;acc:p43897] Ranked 0 16290.7 13464.8 1.20987
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Measured Subtracted 712.071 416.524 295.547
nostrin. [refseq;acc:nm_052946] Ranked 1 209.299 249.187 39.888
nuclear protein ukp68. [refseq;acc:nm_024824] Measured Divided 4241.57 5810.79 1.36996
protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] Rooted 60.8692 77.7165 1.27678
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Measured Subtracted 11068 8508.5 2559.5
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Squared Divided 0 299.137 144.414 2.07139
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Subtracted 1 82624.3 115061 32436.7
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] Measured Divided 0 1251.66 858.525 1.45792
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Rooted Subtracted 13.0522 17.6559 4.6037
transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084] Divided 5.47723 7.07107 1.29099
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Ranked 1 252.329 202.004 1.24913
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Rooted Subtracted 63.7477 48.1589 15.5888
107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Measured Divided 4266.04 5843.51 1.36977
60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 0 1915.27 2206.07 290.8
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Ranked 9183.49 11217.7 2034.21
cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] Squared Divided 1 407289 263351 1.54656
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Rooted Subtracted 0 21.3244 25.9172 4.5928
eap30 subunit of ell complex. [refseq;acc:nm_007241] Ranked 1 209.299 249.187 39.888
fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Rooted Divided 60.875 77.7152 1.27664
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Ranked 252.309 201.998 1.24907
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Measured 0 326.677 472.605 1.4467
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Rooted 22.2259 17.2182 1.29084
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Squared Subtracted 1 84857.8 53402.4 31455.4
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Divided 0 4141.27 2000.69 2.06992
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured Subtracted 1 14229.2 16780.7 2551.5
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Rooted 63.7477 48.1594 15.5883
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Ranked Divided 0 11853.5 9808.86 1.20845
tubby protein homolog. [swissprot;acc:p50607] Squared Subtracted 9661.54 10902.9 1241.36
108 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Ranked 6742.5 8759.5 2017
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Measured Divided 292 421 1.44178
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Squared Subtracted 1797.76 558.241 1239.52
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Rooted Divided 13.7191 17.6786 1.28861
filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Measured 1 4366.44 5899.76 1.35116
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] Ranked 252.296 201.995 1.24902
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] Subtracted 209.299 249.187 39.888
microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] Measured 0 482.426 192.295 290.131
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Squared Divided 1 19321 12542.6 1.54043
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Ranked 0 10585.3 12769.1 1.2063

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/