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 5908 to 5957 of 16578 in total
Value Type  : Measured
Filtered  : 1
Rank
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1477 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Divided Low confidence 7086.97 7329.52 1.03422
1478 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] High confidence 5659.22 6084.68 1.07518
itchy homolog e3 ubiquitin protein ligase; atrophin-1 interacting protein 4; itchy (mouse homolog) e3 ubiquitin protein ligase; nfe2-associated polypeptide 1; ubiquitin protein ligase itch. [refseq;acc:nm_031483] Subtracted 6176.82 6617.91 441.09
protein inhibitor of activated stat x isoform alpha. [refseq;acc:nm_173206] Low confidence 7970.64 8242.52 271.88
ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided 7924.59 8195.68 1.03421
1479 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] 7744.62 8009.5 1.0342
hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317] High confidence 5787.03 6221.72 1.07511
parafibromin. [refseq;acc:nm_024529] Subtracted 4331.17 4771.22 440.05
stress-70 protein, mitochondrial precursor (75 kda glucose regulated protein) (grp 75) (peptide-binding protein 74) (pbp74) (mortalin) (mot). [swissprot;acc:p38646] Low confidence 8068.55 8340.4 271.85
1480 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Divided High confidence 5660.17 6085.22 1.07509
dna replication factor; double parked, drosophila, homolog of. [refseq;acc:nm_030928] Low confidence 7953.27 8225.18 1.03419
jm1 protein. [refseq;acc:nm_014008] Subtracted 7353.1 7624.76 271.66
ubiquitin-like protein sumo-1 conjugating enzyme (ec 6.3.2.19) (sumo- 1-protein ligase) (ubiquitin carrier protein) (ubiquitin-conjugating enzyme ubce2a) (p18). [swissprot;acc:p50550] High confidence 5770.74 6210.65 439.91
1481 dna topoisomerase iii alpha (ec 5.99.1.2). [swissprot;acc:q13472] 5692.34 6131.71 439.37
egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215] Divided 3688.8 3431.33 1.07504
farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324] Low confidence 7915.52 8186.09 1.03418
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [swissprot;acc:p13662] Subtracted 7821.22 8092.78 271.56
1482 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Divided 7871.77 8140.71 1.03417
leng5 protein. [refseq;acc:nm_024075] High confidence 5372.25 5775.21 1.07501
t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559] Subtracted Low confidence 7889.16 8160.65 271.49
ubiquitin. [swissprot;acc:p02248] High confidence 6158.22 6597.55 439.33
1483 serine palmitoyltransferase 1 (ec 2.3.1.50) (long chain base biosynthesis protein 1) (lcb 1) (serine-palmitoyl-coa transferase 1) (spt 1) (spt1). [swissprot;acc:o15269] Divided Low confidence 7774.28 8039.76 1.03415
t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542] Subtracted 7888.9 8160.18 271.28
tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381] Divided High confidence 5372.25 5775.21 1.07501
vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267] Subtracted 6048.57 6487.65 439.08
1484 lyl-1 protein (lymphoblastic leukemia derived sequence 1). [swissprot;acc:p12980] Low confidence 7888.88 8160.14 271.26
mitogen-activated protein kinase kinase kinase 4 (ec 2.7.1.-) (mapk/erk kinase kinase 4) (mek kinase 4) (mekk 4) (map three kinase 1). [swissprot;acc:q9y6r4] Divided 8083.97 8360 1.03415
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] High confidence 5372.25 5775.21 1.07501
vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270] Subtracted 6048.57 6487.65 439.08
1485 double c2-like domains, alpha. [refseq;acc:nm_003586] Low confidence 8136.99 8408.21 271.22
protein inhibitor of activated stat protein 3. [swissprot;acc:q9y6x2] Divided 7970.91 8242.92 1.03413
tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6] High confidence 5372.25 5775.21 1.07501
vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1] Subtracted 6048.57 6487.65 439.08
1486 b/k protein. [refseq;acc:nm_016524] Low confidence 8137.22 8408.44 271.22
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [swissprot;acc:q92831] High confidence 7210.87 7649.23 438.36
t54 protein. [swissprot;acc:q92917] Divided Low confidence 7827.37 8094.52 1.03413
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] High confidence 5372.25 5775.21 1.07501
1487 glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Subtracted 6025.86 6464.16 438.3
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177] Divided 5573.64 5991.58 1.07499
phospholipase d1 (ec 3.1.4.4) (pld 1) (choline phosphatase 1) (phosphatidylcholine-hydrolyzing phospholipase d1) (hpld1). [swissprot;acc:q13393] Low confidence 7867.85 8136.28 1.03412
rabphilin-3a (exophilin 1). [swissprot;acc:q9y2j0] Subtracted 8136.99 8408.21 271.22
1488 cysteine and histidine-rich domain (chord)-containing, zinc binding protein 1; chord domain-containing protein 1; cysteine and histidine-rich domain (chord)-containing, zinc-binding protein 1. [refseq;acc:nm_012124] Divided 7849.85 8117.63 1.03411
delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886] High confidence 5573.64 5991.58 1.07499
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Subtracted 6025.86 6464.16 438.3
double c2-like domains, beta. [refseq;acc:nm_003585] Low confidence 8137.18 8408.39 271.21
1489 dual specificity protein phosphatase 15 (ec 3.1.3.48) (ec 3.1.3.16). [swissprot;acc:q9h1r2] 8171.93 8443.14
general control of amino acid synthesis protein 5-like 2 (ec 2.3.1.-) (histone acetyltransferase gcn5) (hsgcn5). [swissprot;acc:q92830] High confidence 7210.64 7648.94 438.3
protein inhibitor of activated stat x isoform alpha. [refseq;acc:nm_173206] Divided Low confidence 7970.64 8242.52 1.03411
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] High confidence 6192.38 6656.34 1.07492
1490 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Subtracted 6025.86 6464.16 438.3

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/