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 5464 to 5513 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
683 TAF7L tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Rooted Divided 72.8809 78.3254 1.0747
684 no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Subtracted 49.9856 45.4432 4.5424
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Measured 5575.18 6254.85 679.67
ABHD3 alpha/beta hydrolase domain containing protein 3; lung alpha/beta hydrolase 3. [refseq;acc:nm_138340] Squared 23526.4 27879.3 4352.9
EIF3B eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] Measured Divided 4359.82 4880.99 1.11954
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Ranked 132.413 125.389 1.05602
PDK2 [pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [swissprot;acc:q15119] Squared 22328.2 26222.4 1.17441
PFAS phosphoribosylformylglycinamidine synthase (ec 6.3.5.3) (fgam synthase) (fgams) (formylglycinamide ribotide amidotransferase) (fgarat) (formylglycinamide ribotide synthetase). [swissprot;acc:o15067] Ranked Subtracted 223.58 235.027 11.447
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Rooted Divided 72.9862 78.4342 1.07464
685 ATIC bifunctional purine biosynthesis protein purh [includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (ec 2.1.2.3) (aicar transformylase); imp cyclohydrolase (ec 3.5.4.10) (inosinicase) (imp synthetase) (atic)]. [swissprot;acc:p31939] Ranked Subtracted 223.58 235.027 11.447
CDH1 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Rooted 50.4663 45.9313 4.535
HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Divided 57.4644 61.7491 1.07456
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Ranked 132.413 125.389 1.05602
MTX1 metaxin 1. [swissprot;acc:q13505] Measured 9327.58 10442.2 1.1195
SLU7 step ii splicing factor slu7. [refseq;acc:nm_006425] Subtracted 5575.18 6254.85 679.67
TPT1 translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Squared Divided 42363.8 36083.8 1.17404
YIPF5 golgi membrane protein sb140; smooth muscle cell associated protein 5. [refseq;acc:nm_030799] Subtracted 23526.4 27879.3 4352.9
686 no value c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Rooted 50.4666 45.9317 4.5349
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Ranked Divided 132.413 125.389 1.05602
peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521] Squared 28982.3 34012.8 1.17357
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Measured Subtracted 6562.98 7242.37 679.39
ABHD1 alpha/beta hydrolase domain containing protein 1 isoform 2; lung alpha/beta hydrolase protein 1. [refseq;acc:nm_152870] Squared 23526.4 27879.3 4352.9
CLEC3A c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Rooted Divided 86.4264 92.8635 1.07448
PAICS multifunctional protein ade2 [includes: phosphoribosylaminoimidazole- succinocarboxamide synthase (ec 6.3.2.6) (saicar synthetase); phosphoribosylaminoimidazole carboxylase (ec 4.1.1.21) (air carboxylase) (airc)]. [swissprot;acc:p22234] Ranked Subtracted 223.58 235.027 11.447
PRKAG1 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Measured Divided 6920.69 7747.63 1.11949
687 no value ero1-like. [refseq;acc:nm_014584] Subtracted 6562.98 7242.37 679.39
ALDH6A1 methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (ec 1.2.1.27) (mmsdh). [swissprot;acc:q02252] Squared 23526.5 27879.4 4352.9
DMC1 meiotic recombination protein dmc1/lim15 homolog. [swissprot;acc:q14565] Divided 24633.6 28893.6 1.17293
EIF3M dendritic cell protein. [refseq;acc:nm_006360] Ranked Subtracted 223.121 211.685 11.436
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Divided 132.413 125.389 1.05602
N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] Rooted 57.6308 61.9165 1.07436
PRKAA2 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Measured 6920.71 7747.65 1.11949
RPL5 60s ribosomal protein l5. [swissprot;acc:p46777] Rooted Subtracted 50.4641 45.9293 4.5348
688 no value 60s ribosomal protein l23a. [swissprot;acc:p29316] 50.4703 45.9373 4.533
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Divided 60.7997 65.3199 1.07435
AHCY adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526] Squared 22245.5 26087.5 1.17271
CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Ranked Subtracted 223.121 211.685 11.436
HSPE1 10 kda heat shock protein, mitochondrial (hsp10) (10 kda chaperonin) (cpn10). [swissprot;acc:q04984] Squared 23526.4 27879.3 4352.9
POLR2D dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] Ranked Divided 237.554 250.823 1.05586
PRKAA1 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Measured 6920.67 7747.6 1.11949
RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 6311.83 6989.6 677.77
689 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Rooted 67.0234 71.5506 4.5272
CPN1 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Ranked 223.121 211.685 11.436
EIF3M dendritic cell protein. [refseq;acc:nm_006360] Squared Divided 33104 38818.5 1.17262
NFU1 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted 100.684 108.135 1.074
PRKAB2 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Measured 6920.69 7747.63 1.11949
RABAC1 rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Squared Subtracted 23526.4 27879.3 4352.9
RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Measured 6311.6 6989.33 677.73
TCP1 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Ranked Divided 135.379 128.225 1.05579
690 CLEC3B tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Rooted 86.1101 92.4812 1.07399

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/