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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Filtered green Interaction Map Gene red Value Type Network Comparison Type network_comparison Rank description
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Filtered  : 0
green
Interaction Map
red
Value Type
Network Comparison Type
network_comparison
Rank
description
5.39669 High confidence 1.22698 Squared Divided 4.39835 52 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
Subtracted 4.16971 420
33.64 Divided 6.23345 42 nanos (fragment). [sptrembl;acc:q8wy41]
Subtracted 28.2433 358
Low confidence 1.22698 Divided 4.39835 56 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
Subtracted 4.16971 774
5.42219 High confidence 12.5892 Divided 2.32179 91 lats homolog 1. [refseq;acc:nm_004690]
92 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
Subtracted 7.16701 400 lats homolog 1. [refseq;acc:nm_004690]
401 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
Low confidence Divided 2.32179 90 lats homolog 1. [refseq;acc:nm_004690]
91 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
Subtracted 7.16701 761 lats homolog 1. [refseq;acc:nm_004690]
762 sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
5.56738 High confidence 199.549 Measured Divided 35.8425 11 serpin b12. [swissprot;acc:q96p63]
Subtracted 193.982 168
Low confidence Divided 35.8425 10
Subtracted 193.982 280
5.56776 5.83095 Rooted Divided 1.04727 544 adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]
Subtracted 0.26319 768
5.58446 23.0581 Squared Divided 4.12898 61 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
Subtracted 17.4736 732
5.66499 High confidence 9.92134 Rooted Divided 1.75134 43 40s ribosomal protein s26. [swissprot;acc:p02383]
Subtracted 4.25635 115
5.71669 199.249 Measured Divided 34.8539 12 hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
Subtracted 193.532 169
Low confidence Divided 34.8539 11
Subtracted 193.532 281
5.76 High confidence 0.0236686 Squared Divided 243.36 21 succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]
Subtracted 5.73633 407
5.80317 Low confidence 0.0279126 Divided 207.905 15 fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344]
Subtracted 5.77526 766
5.80678 9.84765 Rooted Divided 1.69589 32 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
33 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
34 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
35 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
36 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
37 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
39 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
40 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
41 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
42 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
43 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
44 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
45 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
47 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
48 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
Subtracted 4.04087 196 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
197 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
198 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]

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/