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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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 green network_comparison Gene Interaction Map Value Type Network Comparison Type red Rank description
Results: HTML CSV LaTeX Showing element 601 to 650 of 77072 in total
Filtered  : 0
green
network_comparison
Interaction Map
Value Type
Network Comparison Type
red
Rank
description
6.55744 6.55744 High confidence Rooted Subtracted 0 65 sedlin. [swissprot;acc:o14582]
66 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
655744 Divided 0.00001 11 sedlin. [swissprot;acc:o14582]
12 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
6.80523 1.35766 5.01247 74 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
75 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
1.79276 Subtracted 291 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
292 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
6.85565 1.7443 Divided 11.9583 44 glucosamine-6-phosphate isomerase (ec 3.5.99.6) (glucosamine-6- phosphate deaminase) (gnpda) (glcn6p deaminase) (oscillin). [swissprot;acc:p46926]
Low confidence 29
5.10265 High confidence Subtracted 91
Low confidence 62
5.38516 High confidence Divided 36.9188 21 adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61]
30.0631 Subtracted 3
6.91035 1.38378 Squared Divided 9.56237 216 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
217 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
2.65202 Subtracted 430 high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
431 sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
6.95259 1.26588 Low confidence Rooted Divided 8.80111 110 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]
111 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
1.84852 Subtracted 385 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]
386 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
6.95553 1.26597 Divided 8.80551 109
1.84998 Subtracted 384
6.96286 1.58452 High confidence Divided 11.0328 50 importin 7; ran-binding protein 7. [refseq;acc:nm_006391]
4.06994 Subtracted 126
6.96791 1.25192 Low confidence Divided 8.7233 114 laminin beta-1 chain precursor (laminin b1 chain). [swissprot;acc:p07942]
1.75539 Subtracted 401
6.97663 1.92709 High confidence Divided 3.62029 38 spir-2 protein (fragment). [sptrembl;acc:q8wwl2]
3.35634 Subtracted 157
7.07107 1.29099 Divided 5.47723 106 transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]
Low confidence 100
1.59384 High confidence Subtracted 307
Low confidence 444
7.14143 0.21323 High confidence 6.9282 462 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]
463 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
464 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
465 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
466 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
467 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
468 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
469 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
470 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
471 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
472 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
473 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
474 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
475 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
476 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
477 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]

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/