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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 59524 to 59573 of 66312 in total
Interaction Map  : Low confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
4213 LAMB1 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942] Divided Rooted 71.1753 1.0248 72.9402
NADSYN1 nad synthetase 1; glutamine-dependent nad synthetase. [refseq;acc:nm_018161] Squared 46200.2 1.02559 45047.4
PBX1 pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] Ranked 201.965 1.01007 199.951
Subtracted 2.014
ZNF189 zinc finger protein 189. [swissprot;acc:o75820] Rooted 76.1821 1.8643 78.0464
4214 no value rho interacting protein 3. [refseq;acc:nm_015134] Ranked 202.932 2.014 200.918
ACE angiotensin-converting enzyme, somatic isoform precursor (ec 3.4.15.1) (ace) (dipeptidyl carboxypeptidase i) (kininase ii) (cd143 antigen). [swissprot;acc:p12821] Divided Squared 45124 1.02559 43998.3
CAMK2A calcium/calmodulin-dependent protein kinase type ii alpha chain (ec 2.7.1.123) (cam-kinase ii alpha chain) (cam kinase ii alpha subunit) (camk-ii alpha subunit). [swissprot;acc:q9uqm7] Subtracted 45840.6 1108.5 44732.1
CNOT6L ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571] Divided Ranked 196.65 1.01006 194.692
OXR1 oxidation resistance 1. [refseq;acc:nm_181354] Rooted 73.1905 1.02479 75.0049
SCD acyl-coa desaturase (ec 1.14.19.1) (stearoyl-coa desaturase) (fatty acid desaturase) (delta(9)-desaturase). [swissprot;acc:o00767] Measured 7963.96 1.0202 8124.86
WISP3 wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880] Subtracted 7667.03 171.82 7838.85
ZNF20 zinc finger protein 20 (zinc finger protein kox13) (dkfzp572p0920). [swissprot;acc:p17024] Rooted 76.1821 1.8643 78.0464
4215 no value protein bat5 (hla-b-associated transcript 5) (ng26 protein) (g5) (pp199). [swissprot;acc:o95870] Divided Measured 8302.59 1.0202 8470.34
CAMK2G calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555] Subtracted Squared 45840.4 1108.4 44732
DBNL src homology 3 domain-containing protein hip-55. [refseq;acc:nm_014063] Divided 45807.8 1.02559 44665
LAMB2 laminin beta-2 chain precursor (s-laminin) (laminin b1s chain). [swissprot;acc:p55268] Rooted 71.1658 1.02476 72.9282
LHX4 lim/homeobox protein lhx4. [swissprot;acc:q969g2] Subtracted Measured 8012.62 171.52 8184.14
PBX3 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Divided Ranked 201.978 1.01005 199.969
TRIOBP protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] Subtracted 202.932 2.014 200.918
ZNF132 zinc finger protein 132. [swissprot;acc:p52740] Rooted 76.1821 1.8643 78.0464
4216 no value collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400] Divided Ranked 205.088 1.01004 203.049
BARD1 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] Squared 51462.4 1.02556 52777.9
CCNC cyclin c. [swissprot;acc:p24863] Subtracted Ranked 199.253 2.012 197.241
LDB2 lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Measured 8012.58 171.45 8184.03
MCOLN1 mucolipin 1; mucolipidin. [refseq;acc:nm_020533] Divided Rooted 70.2323 1.02475 71.9703
SALL4 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Measured 7782.77 1.02017 7939.74
SDHA succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] Subtracted Squared 44796.6 1108 43688.6
ZNF304 zinc finger protein 304. [swissprot;acc:q9hcx3] Rooted 76.1821 1.8643 78.0464
4217 no value 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] Divided Measured 8183.95 1.02016 8348.94
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 8012.58 171.45 8184.03
DNA2L dna2-like homolog (dna replication helicase-like homolog) (fragment). [swissprot;acc:p51530] Squared 46191.1 1105.6 45085.5
MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] Ranked 203.661 2.01 201.651
POLR1C dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160] Divided Rooted 71.0944 1.02472 72.8522
SEC16B regucalcin gene promotor region related protein; rgpr-p117. [refseq;acc:nm_033127] Squared 45128.7 1.02551 44005.9
TGS1 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Ranked 206.056 1.01003 204.009
ZNF141 zinc finger protein 141. [swissprot;acc:q15928] Subtracted Rooted 76.1821 1.8643 78.0464
4218 no value rho interacting protein 3. [refseq;acc:nm_015134] Divided Ranked 202.932 1.01002 200.918
GSTZ1 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] Subtracted Measured 7454.64 171.4 7626.04
MTX2 metaxin 2. [swissprot;acc:o75431] Divided Rooted 71.5392 1.0247 73.3063
MYO7A myosin viia. [swissprot;acc:q13402] Measured 8274.94 1.02016 8441.8
PBX3 pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] Subtracted Ranked 201.978 2.009 199.969
RRM2 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Divided Squared 45261.4 1.02546 44137.7
ZMIZ1 retinoic acid induced 17; pias-like protein hzimp10. [refseq;acc:nm_020338] Subtracted 46110.6 1105.1 45005.5
ZNF236 zinc finger protein 236. [swissprot;acc:q9ul36] Rooted 76.182 1.8643 78.0463
4219 no value dead-box protein 3 (helicase-like protein 2) (hlp2) (dead-box, x isoform). [swissprot;acc:o00571] Divided Squared 46040.5 1.02546 44897.5
ANKRD30A breast cancer antigen ny-br-1. [refseq;acc:nm_052997] Subtracted 41059.6 1104.5 39955.1
EIF3J eukaryotic translation initiation factor 3 subunit 1 (eif-3 alpha) (eif3 p35) (eif3j). [swissprot;acc:o75822] Divided Measured 8081.24 1.02014 8244.03
ENDOG endonuclease g, mitochondrial precursor (ec 3.1.30.-) (endo g). [swissprot;acc:q14249] Subtracted Ranked 202.592 2.008 200.584
LHX3 lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Measured 8012.55 171.38 8183.93

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/