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 6908 to 6957 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1727 ras-related protein rab-37. [swissprot;acc:q96ax2] Squared 13960 15382.4 1.10189
1728 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Measured 5475.44 5127.66 1.06782
centaurin gamma 3. [swissprot;acc:q96p47] Rooted 61.1276 63.0891 1.03209
inositol-1(or 4)-monophosphatase 2 (ec 3.1.3.25) (impase 2) (imp 2) (inositol monophosphatase 2) (myo-inositol monophosphatase a2). [swissprot;acc:o14732] Ranked 210.358 213.103 1.01305
ras-related protein rab-26. [swissprot;acc:q9ulw5] Squared 13960 15382.4 1.10189
1729 autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] Ranked 187.582 190.028 1.01304
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Squared 13960 15382.4 1.10189
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Measured 6259.8 6684.31 1.06782
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Rooted 70.2384 72.4913 1.03208
1730 chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60] Ranked 215.336 212.567 1.01303
phospholipid scramblase 4 (pl scramblase 4) (ca(2+)-dependent phospholipid scramblase 4). [swissprot;acc:q9nrq2] Measured 6259.8 6684.3 1.06781
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Rooted 70.2391 72.4922 1.03208
structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945] Squared 18074.5 19915.8 1.10187
1731 aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853] Ranked 215.336 212.567 1.01303
band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2] Rooted 70.2389 72.4919 1.03208
lamin b2. [swissprot;acc:q03252] Measured 5840.77 6236.53 1.06776
sr rich protein. [refseq;acc:nm_032870] Squared 35530.1 32245.4 1.10187
1732 aarf domain containing kinase 4. [refseq;acc:nm_024876] Ranked 215.336 212.567 1.01303
band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Rooted 70.2384 72.4914 1.03208
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192] Squared 18074.5 19915.8 1.10187
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] Measured 5781.8 6173.1 1.06768
1733 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Rooted 70.2391 72.4922 1.03208
aarf domain containing kinase 1. [refseq;acc:nm_020421] Ranked 215.336 212.567 1.01303
elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Measured 5874.83 6272.26 1.06765
mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750] Squared 28523.1 31428.2 1.10185
1734 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] Rooted 70.2384 72.4912 1.03207
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543] Squared 26278.9 28944.8 1.10145
nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838] Ranked 221.921 219.081 1.01296
zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312] Measured 5874.83 6272.26 1.06765
1735 elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Rooted 62.3876 64.3877 1.03206
elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639] Measured 5874.83 6272.26 1.06765
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Squared 26592.4 29289.7 1.10143
leucyl-trna synthetase. [refseq;acc:nm_020117] Ranked 218.99 216.189 1.01296
1736 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Rooted 62.3692 64.3688 1.03206
phd finger protein 9. [refseq;acc:nm_018062] Squared 26592.4 29289.7 1.10143
transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269] Ranked 221.921 219.081 1.01296
twinkle; likely ortholog of mouse t7 gp4-like protein with intramitochondrial nucleoid localization. [refseq;acc:nm_021830] Measured 5925.65 6326.43 1.06763
1737 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] Rooted 62.4076 64.4076 1.03205
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031] Ranked 218.99 216.189 1.01296
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703] Measured 5925.65 6326.43 1.06763
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Squared 26592.4 29289.7 1.10143
1738 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 20110 18258
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] Measured 5885.08 6282.97 1.06761
lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234] Ranked 206.595 209.258 1.01289
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397] Rooted 57.4522 59.2916 1.03202
1739 argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Measured 5695.57 6079.61 1.06743
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Rooted 70.2226 72.4707 1.03201
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] Squared 20103.6 18253.7 1.10134
tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Ranked 206.595 209.258 1.01289
1740 defender against cell death 1 (dad-1). [swissprot;acc:p46966]

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/