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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    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 Gene Value Type Network Comparison Type network_comparison Interaction Map Rank description green red
    Results: HTML CSV LaTeX Showing element 3180 to 3229 of 77072 in total
    Filtered  : 0
    Value Type  : Ranked
    Network Comparison Type  : Divided
    network_comparison
    		Interaction Map
    		Rank
    		description
    		green
    		red
    1.0547 High confidence 338 hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 10571.4 11149.7
    1.0548 Low confidence 518 espin. [refseq;acc:nm_031475] 14545.8 13790.1
    1.055 517 rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] 12854.2 12184.1
    1.0553 516 ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 11832.5 11212.4
    1.0554 515 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 12290.5 11645.4
    1.05541 High confidence 337 glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 12273.2 12953.2
    1.0556 332 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 7697.5 8125.5
    333 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]
    334 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]
    335 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]
    336 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
    1.05594 Low confidence 514 heat shock 70 kda protein 1 (hsp70.1) (hsp70-1/hsp70-2). [swissprot;acc:p08107] 11580 10966.5
    1.05597 513 cg4853 gene product. [refseq;acc:nm_145313] 14671.5 13893.9
    1.05604 512 helicase ski2w (helicase-like protein) (hlp). [swissprot;acc:q15477] 11116.2 10526.3
    1.05644 High confidence 331 40s ribosomal protein s3a. [swissprot;acc:p49241] 10992.4 10405.1
    1.05668 330 pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 13018.5 12320.2
    1.05681 Low confidence 511 zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 10716 11324.8
    1.05701 High confidence 329 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 15115.5 15977.3
    1.05717 328 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] 11520 10897
    1.05727 Low confidence 510 methyltransferase like 2. [refseq;acc:nm_018396] 12508.3 11830.8
    1.05731 509 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] 11175.5 11816
    1.05744 508 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 12764 12070.7
    1.05751 High confidence 327 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 10466.5 9897.29
    1.05772 Low confidence 507 cytochrome p450 3a7 (ec 1.14.14.1) (cypiiia7) (p450-hfla). [swissprot;acc:p24462] 12524.9 11841.4
    1.05779 High confidence 326 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 11295.6 11948.4
    1.05811 325 mstp028 protein. [refseq;acc:nm_031954] 7528.21 7965.66
    Low confidence 506
    1.05843 High confidence 323 ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] 16427.3 17387.1
    324 ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]
    1.05845 Low confidence 505 importin 9. [refseq;acc:nm_018085] 10602 10016.5
    1.05849 504 ero1-like. [refseq;acc:nm_014584] 10148.1 9587.31
    1.05859 502 pnas-18. [sptrembl;acc:q9bzu3] 12793.5 12085.4
    503 neurofibromin (neurofibromatosis-related protein nf-1) [contains: neurofibromin truncated]. [swissprot;acc:p21359] 11516.1 10878.7
    1.05864 High confidence 321 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] 10989.9 11634.4
    322 estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]
    1.0588 Low confidence 501 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] 11352.1 10721.7
    1.05908 499 udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133] 12128.8 12845.4
    500 udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537] 12129.6 12846.2
    1.05928 498 udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310] 12143.1 12862.9
    1.05948 496 udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795] 12162 12885.4
    497 udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855] 12160.8 12884.1
    1.05957 495 dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] 10627.6 11260.7
    1.05985 494 homeobox protein cdx-2 (caudal-type homeobox protein 2) (cdx-3). [swissprot;acc:q99626] 11549.1 12240.3
    1.06002 493 zinc finger protein 232. [swissprot;acc:q9uny5] 10610.1 10009.3
    1.06013 492 lactation elevated 1; cg8520 gene product; lactation elevated-1. [refseq;acc:nm_145315] 9707.52 9156.93
    1.06018 491 ba371l19.2 (novel protein similar to 40s ribosomal protein s10 (rps10)). [sptrembl;acc:q9nq39] 13184 12435.6
    1.06027 490 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] 11010.5 10384.6
    1.06031 489 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 12297 11597.6
    1.06043 488 40s ribosomal protein s10. [swissprot;acc:p46783] 13169.5 12419
    1.06068 487 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 14028.3 14879.6

    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/