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 Rank Network Comparison Type description
Results: HTML CSV LaTeX Showing element 501 to 550 of 77072 in total
Filtered  : 0
green
Interaction Map
red
Value Type
network_comparison
Rank
Network Comparison Type
description
5.39669 High confidence 1.22698 Squared 4.16971 420 Subtracted selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
4.39835 52 Divided
33.64 6.23345 42 nanos (fragment). [sptrembl;acc:q8wy41]
28.2433 358 Subtracted
Low confidence 1.22698 4.16971 774 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]
4.39835 56 Divided
5.42219 High confidence 12.5892 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]
7.16701 400 Subtracted 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 2.32179 90 Divided 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]
7.16701 761 Subtracted 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 35.8425 11 Divided serpin b12. [swissprot;acc:q96p63]
193.982 168 Subtracted
Low confidence 35.8425 10 Divided
193.982 280 Subtracted
5.56776 5.83095 Rooted 0.26319 768 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]
1.04727 544 Divided
5.58446 23.0581 Squared 4.12898 61 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
17.4736 732 Subtracted
5.66499 High confidence 9.92134 Rooted 1.75134 43 Divided 40s ribosomal protein s26. [swissprot;acc:p02383]
4.25635 115 Subtracted
5.71669 199.249 Measured 34.8539 12 Divided hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
193.532 169 Subtracted
Low confidence 34.8539 11 Divided
193.532 281 Subtracted
5.76 High confidence 0.0236686 Squared 5.73633 407 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]
243.36 21 Divided
5.80317 Low confidence 0.0279126 5.77526 766 Subtracted 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]
207.905 15 Divided
5.80678 9.84765 Rooted 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]
4.04087 196 Subtracted 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/