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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene final expected Rank measured description Hugo
Results: HTML CSV LaTeX Showing element 758 to 807 of 3206 in total
final
expected
Rank
measured
description
Hugo
0.217046438 0.345603 2449 0.0750119 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] PGLS
0.21708522 0.94731 2448 0.205647 CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844] ZMPSTE24
0.21709619 2.0418 2447 0.443267 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] HARS2
0.217096399 0.502445 2446 0.109079 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] no value
0.21709644 0.14496 2445 0.0314703 UBL4B
0.217096491 0.536227 2444 0.116413 C7orf20
0.217096516 2.48653 2443 0.539817 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] no value
0.217096709 0.178742 2441 0.0388043 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368]
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
0.217149169 2.33574 2440 0.507204 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS). [SWISSPROT;Acc:P12081] HARS
0.217197827 1.22405 2439 0.265861 GERANYLGERANYL PYROPHOSPHATE SYNTHETASE (GGPP SYNTHETASE) (GGPPSASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10); FARNESYLTRANSTRANSFERASE (EC 2.5.1.29)]. [SWISSPROT; GGPS1
0.21722893 0.563645 2438 0.12244 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] BOLA2B
0.217241069 0.788327 2437 0.171257 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] ANAPC2
0.2172692 0.159272 2436 0.0346049 SETD3
0.217269447 0.725721 2434 0.157677 IMP2 INNER MITOCHONDRIAL MEMBRANE PROTEASE-LIKE; INNER MITOCHONDRIAL MEMBRANE PEPTIDASE 2 LIKE. [RefSeq;Acc:NM_032549] IMMP2L
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] no value
0.217269515 0.884993 2433 0.192282 IMMP1L
0.217417532 0.452567 2432 0.098396 THNSL1
0.217494036 0.657687 2431 0.143043 FIBULIN-1 PRECURSOR. [SWISSPROT;Acc:P23142] FBLN1
0.217496151 0.429323 2430 0.0933761 SIPL PROTEIN. [RefSeq;Acc:NM_018269] ADI1
0.217718168 0.816721 2429 0.177815 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] PLD1
0.21781234 0.672152 2428 0.146403 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] PLD2
0.217873412 1.06471 2427 0.231972 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 (EC 2.7.1.-) (TRANSFORMING GROWTH FACTOR-BETA-ACTIVATED KINASE 1) (TGF-BETA- ACTIVATED KINASE 1). [SWISSPROT;Acc:O43318] MAP3K7
0.217892482 0.670248 2426 0.146042 GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] G6PD
0.21789278 0.335124 2425 0.0730211 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] XRCC3
0.217893078 0.167562 2424 0.0365106 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] RECQL5
0.218132041 0.29203 2423 0.0637011 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] no value
0.218132537 0.258811 2422 0.0564551 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] TCEA2
0.218185932 1.96674 2421 0.429115 FIP1-LIKE 1; REARRANGED IN HYPEREOSINOPHILIA. [RefSeq;Acc:NM_030917] FIP1L1
0.218194818 0.742662 2420 0.162045 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] PCAF
0.218201021 0.669424 2419 0.146069 GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] GCN5L2
0.218346174 2.24292 2418 0.489733 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] PHGDH
0.218346207 0.118068 2417 0.0257797 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] SERINC1
0.218346469 0.136653 2415 0.0298377 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] SERINC3
2416 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272] MAF1
0.218346928 0.114139 2414 0.0249219 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] SERINC2
0.218349163 0.141189 2413 0.030828500000000002 no value
0.218349656 1.63578 2412 0.357172 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] N6AMT1
0.218451681 1.3266 2411 0.289798 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] DCP1A
0.218452136 0.111754 2410 0.0244129 VPS8
0.218734868 0.514239 2409 0.112482 no value
0.218735248 0.845209 2408 0.184877 APIP
0.21873598 0.140868 2407 0.0308129 INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] ITM2B
0.218736385 0.117061 2406 0.0256055 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] ITM2C
0.218736844 0.115441 2405 0.0252512 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] ITM2A
0.218948245 1.22481 2403 0.26817 PROHIBITIN. [SWISSPROT;Acc:P35232] PHB
2404 REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] no value
0.219053357 0.392545 2402 0.0859883 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] NSUN5B
0.219053395 0.366045 2401 0.0801834 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] no value
0.219053571 0.460869 2399 0.100955 WILLIAMS BEUREN SYNDROME CRITICAL REGION 20A ISOFORM 2; NOL1/NOP2/SUN GENE FAMILY MEMBER; WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY A; WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20. [RefSeq;Acc:NM_018044] NSUN5

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
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/