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 5508 to 5557 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
689 hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Rooted Divided 100.684 108.135 1.074
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423] Squared Subtracted 23526.4 27879.3 4352.9
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Measured 6311.6 6989.33 677.73
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Ranked Divided 135.379 128.225 1.05579
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Rooted Subtracted 67.0234 71.5506 4.5272
690 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Measured Divided 6920.69 7747.63 1.11949
60s ribosomal protein l19. [swissprot;acc:p14118] Rooted Subtracted 50.832 46.3081 4.5239
cpz gene product. [refseq;acc:nm_003652] Ranked 223.121 211.685 11.436
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Divided 220.593 208.987 1.05553
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [swissprot;acc:q9y3b8] Squared Subtracted 23526.4 27879.3 4352.9
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Divided 33104 38818.5 1.17262
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Rooted 86.1101 92.4812 1.07399
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Measured Subtracted 6257.99 6932.95 674.96
691 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 6920.69 7747.63 1.11949
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Ranked 217.602 206.195 1.05532
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Subtracted 223.121 211.685 11.436
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] Squared Divided 33104 38818.5 1.17262
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329] Subtracted 23526.5 27879.4 4352.9
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Rooted 60.7997 65.3199 4.5202
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Divided 63.1365 67.8053 1.07395
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Measured Subtracted 8425.35 7751.57 673.78
692 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 6920.69 7747.63 1.11949
autoantigen ngp-1. [swissprot;acc:q13823] Rooted Subtracted 49.4756 53.9896 4.514
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Ranked Divided 217.602 206.195 1.05532
cpz gene product. [refseq;acc:nm_003652] Squared 33104 38818.5 1.17262
e-1 enzyme. [refseq;acc:nm_021204] Measured Subtracted 6603.09 7274.72 671.63
eukaryotic translation initiation factor 3 subunit 4 (eif-3 delta) (eif3 p44) (eif-3 rna-binding subunit) (eif3 p42) (eif3g). [swissprot;acc:o75821] Rooted Divided 51.3598 55.1508 1.07381
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Ranked Subtracted 223.121 211.685 11.436
voltage-gated potassium channel beta-2 subunit (k+ channel beta-2 subunit) (kv-beta-2) (hkvbeta2). [swissprot;acc:q13303] Squared 23526.4 27879.3 4352.9
693 aflatoxin b1 aldehyde reductase 1 (ec 1.-.-.-) (afb1-ar 1) (aldoketoreductase 7). [swissprot;acc:o43488]
breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Ranked 217.602 206.195 11.407
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Squared Divided 33104 38818.5 1.17262
eukaryotic translation initiation factor 3 subunit 10 (eif-3 theta) (eif3 p167) (eif3 p180) (eif3 p185) (eif3a). [swissprot;acc:q14152] Rooted 51.3598 55.1508 1.07381
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured Subtracted 3199.4 3870.8 671.4
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 7725.1 8647.74 1.11943
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Ranked 222.554 234.847 1.05524
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Rooted Subtracted 67.0475 71.5566 4.5091
694 cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Ranked 217.602 206.195 11.407
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Divided 241.907 229.35 1.05475
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Rooted Subtracted 50.0578 54.5502 4.4924
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Measured Divided 7725.1 8647.74 1.11943
importin alpha-1 subunit (karyopherin alpha-1 subunit) (srp1-beta) (rag cohort protein 2) (nucleoprotein interactor 1) (npi-1). [swissprot;acc:p52294] Squared Subtracted 23517.1 27867.3 4350.2
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Measured 6075.55 6746.92 671.37
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Squared Divided 33104 38818.5 1.17262
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Rooted 68.4526 73.4852 1.07352
695 acyl-coenzyme a oxidase 2, peroxisomal (ec 1.3.3.6) (branched-chain acyl-coa oxidase) (brcacox) (trihydroxycoprostanoyl-coa oxidase) (thccox) (thca-coa oxidase). [swissprot;acc:q99424] Squared Subtracted 27382 31722.9 4340.9
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Ranked 210.739 199.398 11.341
peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126] Divided 226.135 214.405 1.05471
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Rooted 63.17 67.8116 1.07348
sphingosine-1-phosphate lyase 1; sphingosine-1-phosphate lyase. [refseq;acc:nm_003901] Squared 22778.5 26693.1 1.17186

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/