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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1363 to 1412 of 25824 in total
Interaction Map	High confidence
Filtered 1
Rank description Value Type Network Comparison Type red green network_comparison 171 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075] Rooted Divided 61.6639 71.7355 1.16333 171 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1] Measured Divided 23693.7 18263 1.29736 171 nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085] Ranked Divided 227.202 192.823 1.17829 171 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [source:swissprot;acc:q9ubn4] Ranked Subtracted 201.478 228.784 27.306 171 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [source:swissprot;acc:p08621] Rooted Subtracted 55.6161 66.7332 11.1171 171 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [source:swissprot;acc:o43623] Squared Subtracted 69165 52991.7 16173.3 172 c-terminal binding protein 1 (ctbp1). [source:swissprot;acc:q13363] Squared Subtracted 69123.3 52967 16156.3 172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902] Ranked Divided 174.667 205.556 1.17685 172 ebp50-pdz interactor of 64 kda (epi64 protein). [source:swissprot;acc:q9bxi6] Ranked Subtracted 201.515 228.752 27.237 172 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [source:swissprot;acc:p21333] Rooted Subtracted 55.6161 66.7332 11.1171 172 likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235] Squared Divided 121579 87259.3 1.39331 172 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007] Measured Subtracted 4556.78 2945.26 1611.52 172 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [source:swissprot;acc:o75533] Rooted Divided 56.7592 65.9889 1.16261 172 trophinin. [source:swissprot;acc:q12816] Measured Divided 23693.7 18263 1.29736 173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5] Rooted Divided 145.551 168.796 1.1597 173 breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567] Measured Divided 4579.34 5940.64 1.29727 173 methyltransferase like 2. [source:refseq;acc:nm_018396] Squared Subtracted 71576.8 56326.7 15250.1 173 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810] Rooted Subtracted 37.3005 48.4141 11.1136 173 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236] Squared Divided 82624.3 115061 1.39258 173 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [source:swissprot;acc:q9ul62] Ranked Subtracted 201.515 228.752 27.237 173 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641] Ranked Divided 227.032 193.056 1.17599 173 uncharacterized hematopoietic stem/progenitor cells protein mds026. [source:sptrembl;acc:q9nz48] Measured Subtracted 4556.79 2945.28 1611.51 174 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [source:swissprot;acc:q15763] Squared Subtracted 71576.8 56326.7 15250.1 174 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [source:swissprot;acc:q96df8] Ranked Divided 335 286 1.17133 174 luc7-like 2; cgi-74 protein; cgi-59 protein. [source:refseq;acc:nm_016019] Ranked Subtracted 228.1 200.968 27.132 174 mad protein (max dimerizer). [source:swissprot;acc:q05195] Measured Divided 4455.95 5774.03 1.2958 174 pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04] Rooted Divided 145.551 168.796 1.1597 174 s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991] Rooted Subtracted 37.3005 48.4141 11.1136 174 sedlin. [source:swissprot;acc:o14582] Squared Divided 112820 157033 1.39189 174 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005] Measured Subtracted 4556.83 2945.38 1611.45 175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [source:refseq;acc:nm_003653] Ranked Divided 199.949 234.187 1.17123 175 f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315] Rooted Subtracted 37.3005 48.4141 11.1136 175 fzr1 protein; fizzy-related protein; cdc20-like 1b. [source:refseq;acc:nm_016263] Squared Subtracted 71576.8 56326.7 15250.1 175 luc7-like; sarcoplasmic reticulum protein luc7b1. [source:refseq;acc:nm_018032] Ranked Subtracted 228.085 201.006 27.079 175 max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539] Measured Divided 4456.67 5773.77 1.29553 175 pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23] Rooted Divided 145.551 168.796 1.1597 175 serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4] Measured Subtracted 4556.99 2945.8 1611.19 175 synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296] Squared Divided 112820 157033 1.39189 176 bet3 homolog. [source:swissprot;acc:o43617] Squared Divided 112820 157033 1.39189 176 cullin homolog 2 (cul-2). [source:swissprot;acc:q13617] Rooted Subtracted 37.3005 48.4141 11.1136 176 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33] Ranked Divided 275.754 235.908 1.1689 176 eukaryotic translation initiation factor 5 (eif-5). [source:swissprot;acc:p55010] Ranked Subtracted 271.016 244.167 26.849 176 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [source:swissprot;acc:p00492] Measured Subtracted 10235.2 11830.8 1595.6 176 max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582] Measured Divided 4456.93 5773.67 1.29544 176 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999] Rooted Divided 145.551 168.796 1.1597 176 proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [source:swissprot;acc:q92824] Squared Subtracted 71576.8 56326.7 15250.1 177 beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121] Squared Subtracted 9924.76 25146.6 15221.8 177 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [source:sptrembl;acc:q8wwk2] Ranked Divided 229.406 196.695 1.1663 177 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [source:refseq;acc:nm_022075] Measured Subtracted 4110.14 5694.99 1584.85 177 max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300] Measured Divided 4457.06 5773.63 1.29539 Legend: - Rank is the rank after comparing the two networks - 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/