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 1425 to 1474 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
713 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted 5162.52 5822.47 659.95
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Divided 3996.81 4465.61 1.11729
714 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 5222.71 5834.57 1.11715
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Subtracted 5873.77 6532.44 658.67
715 dendritic cell protein. [refseq;acc:nm_006360] Divided 6593.17 7364.55 1.117
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 5874.74 6533.34 658.6
716 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Divided 6593.17 7364.55 1.117
717 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]
sec13-related protein. [swissprot;acc:p55735] Subtracted 5874.76 6533.36 658.6
718 cpz gene product. [refseq;acc:nm_003652] Divided 6593.17 7364.55 1.117
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Subtracted 5874.74 6533.34 658.6
719 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Divided 6593.17 7364.55 1.117
yeast sec31p homolog. [refseq;acc:nm_014933] Subtracted 5874.76 6533.36 658.6
720 ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Divided 6593.17 7364.55 1.117
721 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Subtracted 5874.74 6533.34 658.6
syntaxin 7. [swissprot;acc:o15400] Divided 5580.97 6233.52 1.11692
722 histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590] 8061.05 9002.33 1.11677
vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313] Subtracted 5874.63 6533.23 658.6
723 ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972] 5874.76 6533.36
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081] Divided 8056.09 8996.46 1.11673
724 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 5384.41 6012.82 1.11671
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8] Subtracted 5874.76 6533.36 658.6
725 phenylalanine-trna synthetase. [refseq;acc:nm_006567] Divided 5384.41 6012.82 1.11671
secretory pathway component sec31b-1. [refseq;acc:nm_015490] Subtracted 5874.76 6533.36 658.6
726 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] Divided 6327.86 7064.13 1.11635
vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281] Subtracted 5874.78 6533.37 658.59
727 60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Divided 7087.23 7911.25 1.11627
vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] Subtracted 5874.74 6533.33 658.59
728 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Divided 6000.23 6696.89 1.11611
vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543] Subtracted 5874.77 6533.36 658.59
729 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 6000.23 6696.89 1.11611
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12] Subtracted 5874.74 6533.33 658.59
730 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Divided 6000.23 6696.89 1.11611
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Subtracted 6276.97 6934.8 657.83
731 dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]
methyltransferase like 2. [refseq;acc:nm_018396] Divided 13241.4 11864 1.1161
732 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Subtracted 5890.49 6547.9 657.41
733 fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Divided 13241.4 11864 1.1161
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Subtracted 5890.41 6547.81 657.4
734 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632] 5890.59 6547.99
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] Divided 13241.4 11864 1.1161
735 vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 5768.32 6434.78 1.11554
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Subtracted 5890.88 6548.28 657.4
736 sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Divided 5768.32 6434.78 1.11554
translation initiation factor if-2. [swissprot;acc:o60841] Subtracted 5811.51 6467.62 656.11
737 atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049] 6000.07 6655.11 655.04
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Divided 5768.32 6434.78 1.11554

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/