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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Gene Rank description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1850 to 1899 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
925 phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Low confidence 201.128 196.213 1.02505
926 glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104] 201.442 196.519
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] High confidence 217.942 210.139 1.03713
927 ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Low confidence 198.264 193.42 1.02504
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] High confidence 217.942 210.139 1.03713
928 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] 225.976 218.017 1.03651
transcription factor etv6 (ets-related protein tel1) (tel) (ets translocation variant 6). [swissprot;acc:p41212] Low confidence 205.137 200.128 1.02503
929 homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] 198.26 193.418
mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] High confidence 225.955 218.015 1.03642
930 protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284] Low confidence 205.137 200.128 1.02503
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] High confidence 231.357 239.778 1.0364
931 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 164.917 1.03637
transcription factor tel-2 (ets-related protein tel2) (tel related ets factor). [swissprot;acc:q9y603] Low confidence 205.137 200.128 1.02503
932 fructose-1,6-bisphosphatase (ec 3.1.3.11) (d-fructose-1,6-bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:p09467] 190.502 185.852 1.02502
mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] High confidence 225.939 218.013 1.03636
933 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] 159.165 164.951 1.03635
dj842g6.2 (novel protein imilar to sel1l (sel-1 (suppressor of lin-12, c.elegans)-like)) (fragment). [sptrembl;acc:q9ugd3] Low confidence 190.447 185.802 1.025
934 nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917] High confidence 242.024 233.544 1.03631
sel-1 homolog precursor (suppressor of lin-12-like protein) (sel-1l). [swissprot;acc:q9ubv2] Low confidence 190.447 185.803 1.02499
935 immature colon carcinoma transcript 1 (digestion substraction 1) (ds- 1). [swissprot;acc:q14197] 200.801 195.908 1.02498
sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] High confidence 232.473 224.372 1.03611
936 casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] Low confidence 190.386 185.747 1.02497
937 spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] 194.236 189.504
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] High confidence 220.246 212.618 1.03588
938 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Low confidence 203.609 198.648 1.02497
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] High confidence 220.246 212.618 1.03588
939 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] 216.501 224.27
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Low confidence 206.817 201.78 1.02496
940 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] High confidence 212.442 205.088 1.03586
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Low confidence 202.747 197.81 1.02496
941 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 207.026 201.99 1.02493
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] High confidence 212.437 205.083 1.03586
942 grancalcin. [swissprot;acc:p28676] 212.442 205.088
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Low confidence 207.862 202.809 1.02492
943 nadh-ubiquinone oxidoreductase sgdh subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-sgdh) (ci-sgdh). [swissprot;acc:o43674] 205.602 200.603
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] High confidence 212.442 205.087 1.03586
944 growth hormone inducible transmembrane protein (dermal papilla derived protein 2) (my021 protein) (ptd010). [swissprot;acc:q9h3k2] Low confidence 204.752 199.775 1.02491
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] High confidence 212.437 205.083 1.03586
945 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 212.44 205.085
sedlin. [swissprot;acc:o14582] Low confidence 195.693 190.937 1.02491
946 histone h4. [swissprot;acc:p02304] High confidence 227.765 219.902 1.03576
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Low confidence 204.752 199.775 1.02491
947 ad24 protein. [refseq;acc:nm_022451] 203.472 198.533 1.02488
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 212.51 205.191 1.03567
948 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Low confidence 209.239 204.165 1.02485
target of myb protein 1. [swissprot;acc:o60784] High confidence 217.254 209.824 1.03541
949 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Low confidence 204.147 199.196 1.02485
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] High confidence 217.253 209.826 1.0354
950 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Low confidence 204.147 199.196 1.02485

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/