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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Network Comparison Type Gene Value Type green description Rank network_comparison red Filtered Interaction Map
Results: HTML CSV LaTeX Showing element 1027 to 1076 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Interaction Map  : High confidence
green
description
Rank
network_comparison
red
202.54 transcription factor relb (i-rel). [swissprot;acc:q01201] 2615 1.00139 202.821
202.646 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 81 1.25645 254.614
202.668 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 77 1.2567 254.692
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 79 254.693
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 80 1.25669 254.691
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 78 1.2567 254.693
202.726 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] 1484 1.0191 198.927
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] 1483
202.739 sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] 2000 1.00931 204.626
202.748 solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] 1999 204.636
202.759 kidney and liver proline oxidase 1. [refseq;acc:nm_021232] 1997 1.00933 204.651
202.784 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 1996 1.00936 204.682
202.925 tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] 2321 1.00485 203.909
202.948 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 2674 1.001 203.151
203.109 peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] 1147 1.02729 208.651
203.183 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 1100 1.02889 209.052
203.208 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 1097 1.02911 209.123
203.235 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 284 1.10541 224.657
203.237 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 762 1.0493 213.256
203.242 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 285 1.10532 224.647
203.251 enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 286 1.1052 224.633
203.303 signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] 761 1.0493 213.325
203.437 tripartite motif protein 2. [swissprot;acc:q9c040] 2268 1.00556 202.312
203.485 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 1749 1.01264 206.058
203.518 ubiquitin. [swissprot;acc:p02248] 1148 1.02724 209.061
203.553 sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 1718 1.01325 206.251
203.57 alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911] 2255 1.00595 202.366
203.691 tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382] 2233 1.00631 202.414
203.748 transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] 2442 1.00329 204.419
203.787 ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112] 2681 1.00096 203.592
203.8 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 721 1.0538 214.765
203.814 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 865 1.03997 211.961
203.818 sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] 1716 1.01327 206.522
203.832 transcription factor btf3 homolog 3. [swissprot;acc:q13892] 870 1.03962 211.908
203.844 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 1714 1.01327 206.549
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] 1715
203.873 trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] 1951 1.00982 205.876
203.874 bag-family molecular chaperone regulator-2. [swissprot;acc:o95816] 1785 1.01206 206.332
homeobox protein meis1. [swissprot;acc:o00470] 1783
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770] 1784
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687] 1788
hyporthetical protein mgc27169. [refseq;acc:nm_176782] 1782
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245] 1787
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424] 1779
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425] 1786
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426] 1781
203.877 germ cell-less. [refseq;acc:nm_022471] 1780 206.335
203.954 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] 879 1.03946 212.002
5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] 877
5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] 876

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/