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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Filtered Gene green Network Comparison Type Rank Interaction Map red Value Type description network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Filtered  : 0
green
Network Comparison Type
Rank
Interaction Map
red
Value Type
description
network_comparison
5.80678 Subtracted 199 Low confidence 9.84765 Rooted melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 4.04087
200 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
201 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
202 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
203 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
204 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
205 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
206 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
207 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
208 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
209 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
210 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]
5.80679 Divided 38 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 1.69589
46 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
Subtracted 211 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 4.04086
212 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
5.86733 Divided 206 High confidence 8.27667 Squared small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678] 1.41064
Subtracted 434 2.40934
5.87091 Divided 41 3.30572 Rooted suppressor of actin 1. [refseq;acc:nm_014016] 1.77599
Subtracted 218 2.56519
5.90479 Divided 119 4.72248 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 1.25036
Subtracted 351 1.18231
5.90864 Divided 17 Low confidence 0.213018 Squared ptd016 protein. [refseq;acc:nm_016125] 27.7377
28 High confidence
Subtracted 408 5.69562
767 Low confidence
5.9911 Divided 114 11.4237 protein tyrosine phosphatase type iva, member 2 isoform 1; protein tyrosine phosphatase iva2; protein tyrosine phosphatase iva; phosphatase of regenerating liver 2. [refseq;acc:nm_003479] 1.90678
Subtracted 768 5.4326
6.06104 Divided 110 High confidence 7.7419 Rooted protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 1.27732
Subtracted 299 1.68086
6.08276 Divided 87 Low confidence 8.12404 arf gtpase-activating protein. [refseq;acc:nm_133446] 1.33558
88 up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
Subtracted 365 arf gtpase-activating protein. [refseq;acc:nm_133446] 2.04128
366 up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707]
6.15501 Divided 62 High confidence 21.2079 Squared elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] 3.44563
Subtracted 386 15.0529
6.23127 Divided 59 4.28588 Rooted metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 1.45391
62 Low confidence
Subtracted 281 High confidence 1.94539
375 Low confidence
6.30196 Divided 478 High confidence 6.24948 adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377] 1.0084
Subtracted 486 0.05248
6.32456 Divided 589 Low confidence 6.55744 probable mitochondrial import receptor subunit tom7 homolog (translocase of outer membrane 7 kda subunit homolog) (protein ad- 014). [swissprot;acc:q9p0u1] 1.03682
Subtracted 776 0.23288
6.488 Divided 112 8.14325 sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983] 1.25512
Subtracted 436 1.65525
6.50325 Divided 14 High confidence 130.512 Measured cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 20.0687
Subtracted 258 124.009
6.55744 Divided 11 0.00001 Rooted sedlin. [swissprot;acc:o14582] 655744
12 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]

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/