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 2080 to 2129 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
260 surfeit locus protein 5. [swissprot;acc:q15528] Ranked Subtracted 242.14 265.696 23.556
261 carboxypeptidase a5. [refseq;acc:nm_080385] Squared 53174 44377.4 8796.6
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 9.1541
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked Divided 219.421 196.978 1.11394
pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Rooted 62.3337 70.0738 1.12417
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured 4247.36 5192.61 1.22255
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 4571.89 5864.86 1292.97
zinc finger protein 291. [swissprot;acc:q9by12] Ranked 242.14 265.696 23.556
262 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Squared 53174 44377.4 8796.6
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693] Measured Divided 24896.4 20431.7 1.21852
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared 26157.6 20236.2 1.29261
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured Subtracted 4571.89 5864.86 1292.97
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Ranked 242.14 265.696 23.556
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted Divided 59.4073 66.7002 1.12276
rna-binding protein. [refseq;acc:nm_019027] Subtracted 52.7642 61.9019 9.1377
263 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Squared Divided 26157.6 20236.2 1.29261
apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Rooted Subtracted 52.7642 61.9019 9.1377
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Measured 4571.89 5864.86 1292.97
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked Divided 219.421 196.978 1.11394
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Squared Subtracted 53174 44377.4 8796.6
paxillin. [swissprot;acc:p49023] Rooted Divided 59.4073 66.7002 1.12276
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked Subtracted 242.14 265.696 23.556
trs85 homolog. [swissprot;acc:q9y2l5] Measured Divided 24896.4 20431.7 1.21852
264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] Ranked Subtracted 243.24 266.796 23.556
adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Squared Divided 26157.6 20236.2 1.29261
aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Subtracted 53174 44377.4 8796.6
cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured Divided 4987.58 4094.57 1.2181
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 12503.3 11212 1291.3
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked Divided 219.421 196.978 1.11394
ns1-associated protein 1. [refseq;acc:nm_006372] Rooted Subtracted 52.7642 61.9019 9.1377
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 66.1122 74.1438 1.12148
265 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked Subtracted 240.243 263.798 23.555
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 8796.6
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted 52.7642 61.9019 9.1377
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared Divided 26157.6 20236.2 1.29261
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Measured Subtracted 4638.1 5923.4 1285.3
Ranked Divided 225.217 202.459 1.11241
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
266 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Rooted Subtracted 52.7702 61.8915 9.1213
fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Squared Divided 26157.6 20236.2 1.29261
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Subtracted 59335 68062.6 8727.6
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted Divided 66.1064 74.1074 1.12103
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Ranked Subtracted 243.12 266.662 23.542
solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Measured 11222.2 9948.93 1273.27
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked Divided 241.07 267.88 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 266.661 23.541

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/