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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description Rank Gene Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 651 to 700 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
description
Rank
red
green
network_comparison
crk-like protein. [swissprot;acc:p46109] 552 207.26 194.346 1.06645
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 564 220.744 207.121 1.06577
ctcl tumor antigen l14-2. [refseq;acc:nm_018017] 2846 0.00001 0.00001 1
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] 1755 180.609 178.393 1.01242
cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] 1801 217.984 215.441 1.0118
cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] 1804 215.442
cullin homolog 1 (cul-1). [swissprot;acc:q13616] 212 285.684 252.234 1.13261
cullin homolog 2 (cul-2). [swissprot;acc:q13617] 210
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 1401 218.657 214.11 1.02124
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 28 201.949 153.671 1.31416
cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850] 1683 216.899 213.889 1.01407
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941] 1680
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 1400 218.667 214.118 1.02125
cyclin c. [swissprot;acc:p24863] 1812 217.071 214.564 1.01168
cyclin g1 (cyclin g). [swissprot;acc:p51959] 963 130.066 134.527 1.0343
cyclin g2. [swissprot;acc:q16589] 962
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946] 2983 0.00001 0.00001 1
cyclin k. [swissprot;acc:o75909] 3160
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348] 2606 214.5 214.198 1.00141
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649] 2604 214.486 214.184
cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623] 2601 214.502 214.2
cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184] 2603 214.494 214.192
cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563] 3002 0.00001 0.00001 1
cyclin t2. [swissprot;acc:o60583] 3171
cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076] 2892
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 336 312 284 1.09859
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 1452 160.381 163.554 1.01978
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 1833 180.409 182.459 1.01136
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247] 2570 219.907 220.267 1.00164
cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622] 2938 0.00001 0.00001 1
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 1022 205.632 199.266 1.03195
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 121 269.254 327.655 1.2169
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 14 56.6768 75.3531 1.32952
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] 17 56.7841 75.447 1.32866
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441] 1531 217.025 213.304 1.01744
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 230 239.35 267.915 1.11934
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 1423 221.152 216.659 1.02074
cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107] 3018 0.00001 0.00001 1
cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108] 3150
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320] 1880 220.852 223.225 1.01074
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] 1757 180.537 178.325 1.0124
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243] 1862 210.856 213.147 1.01087
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229] 1861
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1] 1511 213.268 209.509 1.01794
cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674] 2791 0.00001 0.00001 1
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854] 3009
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073] 2402 182.4 183.083 1.00374
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9] 2403
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] 1369 228.644 223.736 1.02194
cytochrome c. [swissprot;acc:p00001] 1533 228.419 232.376 1.01732

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/