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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2082 to 2131 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
261 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted Subtracted 52.7582 61.9123 9.1541
HS3ST3A1 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
PC pyruvate carboxylase, mitochondrial precursor (ec 6.4.1.1) (pyruvic carboxylase) (pcb). [swissprot;acc:p11498] Squared 48127.9 62245.6 1.29334
RRM2B 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
SCAPER zinc finger protein 291. [swissprot;acc:q9by12] Ranked Subtracted 242.14 265.696 23.556
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Measured Divided 4247.36 5192.61 1.22255
STT3B source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Subtracted 4571.89 5864.86 1292.97
262 no value rna-binding protein. [refseq;acc:nm_019027] Rooted 52.7642 61.9019 9.1377
CHRNA7 neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Squared Divided 26157.6 20236.2 1.29261
CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Subtracted 53174 44377.4 8796.6
CPSF4 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
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 1.11394
PEX1 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] Subtracted 242.14 265.696 23.556
POLI 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
STT3A oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Measured Subtracted 4571.89 5864.86 1292.97
263 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Rooted 52.7642 61.9019 9.1377
ADCY6 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
DDOST 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 Subtracted 4571.89 5864.86 1292.97
HS3ST2 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
KIAA1012 trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 20431.7 1.21852
PXN paxillin. [swissprot;acc:p49023] Rooted 59.4073 66.7002 1.12276
SLC3A1 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
TXNDC9 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Ranked 242.14 265.696 23.556
264 no value 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796
ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Squared 53174 44377.4 8796.6
ADCY5 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Divided 26157.6 20236.2 1.29261
COPS3 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Measured 4987.58 4094.57 1.2181
CTPS ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] Subtracted 12503.3 11212 1291.3
DCPS 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
SYNCRIP ns1-associated protein 1. [refseq;acc:nm_006372] Rooted Subtracted 52.7642 61.9019 9.1377
WAS wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 66.1122 74.1438 1.12148
265 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked Subtracted 240.243 263.798 23.555
CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 8796.6
HNRNPR heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390] Rooted 52.7642 61.9019 9.1377
LRRC15 leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Squared Divided 26157.6 20236.2 1.29261
LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Rooted 56.031 62.8281 1.12131
SF3B1 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
WDR33 wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 1.21782
266 CPSF1 cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
CRK proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Rooted 66.1064 74.1074 1.12103
EIF4G1 eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637] Subtracted 52.7702 61.8915 9.1213
FEM1B 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
HNRNPL heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866] Subtracted 59335 68062.6 8727.6
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Ranked 243.12 266.662 23.542
SIN3A transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 241.07 267.88 1.11121
SLC4A1AP 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 Subtracted 11222.2 9948.93 1273.27
267 no value 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Ranked 243.12 266.661 23.541
estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] Squared 59334.6 68040.1 8705.5
ABL2 tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted Divided 66.1064 74.1073 1.12103

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
- Hugo is the HGNC identifier if it exists
- 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/