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 910 to 959 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
114 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Squared 1 19321 12542.6 1.54043
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] Rooted 0 14.7363 18.7165 1.27009
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Squared 35.0828 69.7867 1.9892
115 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Measured 1 21185 28492 1.34491
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared 0 105.615 53.4024 1.97772
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 1 19321 12542.6 1.54043
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Rooted 0 18.4959 14.5738 1.26912
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Ranked 1 332.874 267.246 1.24557
spermatogenesis associated 6. [refseq;acc:nm_019073] Rooted 80.4705 101.526 1.26165
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Ranked 0 18662.8 15627 1.19427
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Measured 385 543 1.41039
116 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 668 475 1.40632
amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Rooted 1 80.4705 101.526 1.26165
dead-box protein. [refseq;acc:nm_018665] Squared 0 37.7545 19.3759 1.94853
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Rooted 9.7842 7.75282 1.26202
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Ranked 1 268.565 334.483 1.24545
metaxin 1. [swissprot;acc:q13505] 0 13761.3 16422.1 1.19335
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 1 19321 12542.6 1.54043
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Measured 21185 28492 1.34491
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] Ranked 0 11545 13771.5 1.19285
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Squared 1 211446 137422 1.53866
neuralized-like. [refseq;acc:nm_004210] Ranked 332.326 266.948 1.24491
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Measured 21185 28492 1.34491
peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Rooted 0 26.63 33.5888 1.26131
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] Squared 0.545459 1.05706 1.93793
transcription factor jun-b. [swissprot;acc:p17275] Rooted 1 63.4173 79.5311 1.25409
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 0 170.5 122 1.39754
118 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Ranked 12049 14370.7 1.19269
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] Rooted 1 50.3065 62.9788 1.2519
methyltransferase like 2. [refseq;acc:nm_018396] Measured 0 31 43 1.3871
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] Rooted 9.1258 11.4849 1.25851
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Ranked 1 284.753 228.934 1.24382
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Measured 21185 28492 1.34491
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Squared 210445 136779 1.53858
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 240.689 124.83 1.92813
119 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Measured 633.85 460.2 1.37734
exocyst complex component sec5. [swissprot;acc:q96kp1] Squared 1 210335 136716 1.53848
mesoderm induction early response 1. [refseq;acc:nm_020948] Ranked 0 3609 4302.5 1.19216
methyltransferase like 2. [refseq;acc:nm_018396] Squared 0.227456 0.437633 1.92403
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Measured 1 21185 28492 1.34491
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] Ranked 318.982 259.004 1.23157
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 0 4.72248 5.90479 1.25036
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 1 50.3247 62.9892 1.25166
120 dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] 0 22.9115 28.547 1.24597
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] Measured 1 5136.78 6895.98 1.34247
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Rooted 50.3333 62.9942 1.25154
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared 210199 136638 1.53836
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Ranked 269.278 327.709 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 5797 4873 1.18962
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Measured 494.417 359.631 1.37479

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/