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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 4208 to 4257 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
1052 TRPC5 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided Low confidence 200.439 205.267 1.02409
1053 no value spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Subtracted 194.236 189.504 4.732
ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] High confidence 219.655 213.385 6.27
LARP4 c-mpl binding protein. [refseq;acc:nm_052879] Divided Low confidence 204.184 199.387 1.02406
PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] High confidence 207.04 200.84 1.03087
1054 no value 60s ribosomal protein l21. [swissprot;acc:p46778] 223.958 217.263 1.03082
PSMA5 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Subtracted 207.04 200.84 6.2
RUNX2 runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950] Divided Low confidence 210.793 205.841 1.02406
VAPA vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0] Subtracted 204.256 199.524 4.732
1055 ASNSD1 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Divided High confidence 219.01 212.468 1.03079
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Subtracted 138.705 132.538 6.167
NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided Low confidence 199.656 194.966 1.02406
TRIB3 neuronal cell death inducible putative kinase (skip3). [swissprot;acc:q96ru7] Subtracted 203.522 198.791 4.731
1056 no value methyltransferase like 2. [refseq;acc:nm_018396] High confidence 147.211 153.371 6.16
ATP6V1A vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Divided 219.01 212.468 1.03079
FARS2 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Low confidence 202.569 197.815 1.02403
TRIB1 g-protein-coupled receptor induced protein. [refseq;acc:nm_025195] Subtracted 203.52 198.79 4.73
1057 ASNS asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Divided High confidence 219.01 212.468 1.03079
CPT1C carnitine palmitoyltransferase i related c. [refseq;acc:nm_152359] Subtracted Low confidence 203.519 198.789 4.73
DYNLT1 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] High confidence 147.211 153.371 6.16
FARSB phenylalanyl-trna synthetase beta chain (ec 6.1.1.20) (phenylalanine-- trna ligase beta chain) (phers) (hspc173). [swissprot;acc:q9nsd9] Divided Low confidence 202.569 197.815 1.02403
1058 ATXN2L ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] High confidence 228.105 221.293 1.03078
CPT1A carnitine o-palmitoyltransferase i, mitochondrial liver isoform (ec 2.3.1.21) (cpt i) (cpti-l). [swissprot;acc:p50416] Subtracted Low confidence 203.519 198.789 4.73
FZR1 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] High confidence 147.211 153.371 6.16
TRAPPC1 bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8] Divided Low confidence 198.804 194.142 1.02401
1059 no value ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] High confidence 228.105 221.293 1.03078
KDELR2 er lumen protein retaining receptor 2 (kdel receptor 2) (elp-1). [swissprot;acc:p33947] Subtracted Low confidence 202.92 198.191 4.729
PCSK5 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] High confidence 147.211 153.371 6.16
SLC7A4 cationic amino acid transporter-4 (cat-4) (cat4). [swissprot;acc:o43246] Divided Low confidence 200.552 195.852 1.024
1060 KDELR1 er lumen protein retaining receptor 1 (kdel receptor 1). [swissprot;acc:p24390] Subtracted 202.92 198.191 4.729
NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Divided High confidence 218.162 211.648 1.03078
SEPT6 septin 6. [swissprot;acc:q14141] Subtracted 126.604 120.463 6.141
SYT12 synaptotagmin xii (sytxii). [swissprot;acc:q8iv01] Divided Low confidence 203.527 198.76 1.02398
1061 AP3M1 adapter-related protein complex 3 mu 1 subunit (mu-adaptin 3a) (ap-3 adapter complex mu3a subunit). [swissprot;acc:q9y2t2] Subtracted High confidence 217.323 211.185 6.138
ERC1 elks protein. [refseq;acc:nm_015064] Divided 218.162 211.648 1.03078
TRIB2 tribbles homolog 2. [refseq;acc:nm_021643] Subtracted Low confidence 203.515 198.787 4.728
YBX2 germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982] Divided 204.104 199.324 1.02398
1062 no value dna-crosslink repair gene snm1. [refseq;acc:nm_014881] 203.048 198.295 1.02397
BRP44 brain protein 44. [swissprot;acc:o95563] Subtracted High confidence 126.215 120.078 6.137
EIF3C eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Low confidence 202.98 198.253 4.727
ZNF174 zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Divided High confidence 269.963 278.239 1.03066
1063 no value t-cell activation protein phosphatase 2c. [refseq;acc:nm_139283] Low confidence 203.048 198.295 1.02397
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Subtracted 196.475 191.748 4.727
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided High confidence 269.96 278.232 1.03064
SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Subtracted 126.215 120.078 6.137
1064 AP3M2 adapter-related protein complex 3 mu 2 subunit (clathrin coat assembly protein ap47 homolog 2) (clathrin coat associated protein ap47 homolog 2) (golgi adaptor ap-1 47 kda protein homolog 2) (ha1 47 kda subunit homolog 2) (clathrin assembly protein assembly protein complex 1 medium chain homolog 2) (p47b). [swissprot;acc:p53677] 217.315 211.183 6.132
COQ7 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] Divided Low confidence 201.995 197.269 1.02396
ETFDH electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial precursor (ec 1.5.5.1) (etf-qo) (etf-ubiquinone oxidoreductase) (etf dehydrogenase) (electron-transferring- flavoprotein dehydrogenase). [swissprot;acc:q16134] Subtracted 198.075 193.349 4.726
ZNF24 zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Divided High confidence 269.955 278.221 1.03062
1065 ABCF2 atp-binding cassette, sub-family f, member 2 (iron inhibited abc transporter 2) (hussy-18). [swissprot;acc:q9ug63] Low confidence 201.115 196.411 1.02395

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/