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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Rank Gene description measured expected final Hugo
Results: HTML CSV LaTeX Showing element 2401 to 2450 of 3206 in total
Rank
description
measured
expected
final
Hugo
2401 WILLIAMS-BEUREN SYNDROME CRITICAL REGION PROTEIN 20 COPY B. [RefSeq;Acc:NM_145645] 0.0801834 0.366045 0.219053395 no value
2402 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] 0.0859883 0.392545 0.219053357 NSUN5B
2403 PROHIBITIN. [SWISSPROT;Acc:P35232] 0.26817 1.22481 0.218948245 PHB
2404 REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] no value
2405 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] 0.0252512 0.115441 0.218736844 ITM2A
2406 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] 0.0256055 0.117061 0.218736385 ITM2C
2407 INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] 0.0308129 0.140868 0.21873598 ITM2B
2408 0.184877 0.845209 0.218735248 APIP
2409 0.112482 0.514239 0.218734868 no value
2410 0.0244129 0.111754 0.218452136 VPS8
2411 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] 0.289798 1.3266 0.218451681 DCP1A
2412 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 0.357172 1.63578 0.218349656 N6AMT1
2413 0.030828500000000002 0.141189 0.218349163 no value
2414 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.0249219 0.114139 0.218346928 SERINC2
2415 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.0298377 0.136653 0.218346469 SERINC3
2416 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272] MAF1
2417 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.0257797 0.118068 0.218346207 SERINC1
2418 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] 0.489733 2.24292 0.218346174 PHGDH
2419 GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] 0.146069 0.669424 0.218201021 GCN5L2
2420 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] 0.162045 0.742662 0.218194818 PCAF
2421 FIP1-LIKE 1; REARRANGED IN HYPEREOSINOPHILIA. [RefSeq;Acc:NM_030917] 0.429115 1.96674 0.218185932 FIP1L1
2422 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] 0.0564551 0.258811 0.218132537 TCEA2
2423 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 0.0637011 0.29203 0.218132041 no value
2424 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] 0.0365106 0.167562 0.217893078 RECQL5
2425 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] 0.0730211 0.335124 0.21789278 XRCC3
2426 GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] 0.146042 0.670248 0.217892482 G6PD
2427 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] 0.231972 1.06471 0.217873412 MAP3K7
2428 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] 0.146403 0.672152 0.21781234 PLD2
2429 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.177815 0.816721 0.217718168 PLD1
2430 SIPL PROTEIN. [RefSeq;Acc:NM_018269] 0.0933761 0.429323 0.217496151 ADI1
2431 FIBULIN-1 PRECURSOR. [SWISSPROT;Acc:P23142] 0.143043 0.657687 0.217494036 FBLN1
2432 0.098396 0.452567 0.217417532 THNSL1
2433 0.192282 0.884993 0.217269515 IMMP1L
2434 IMP2 INNER MITOCHONDRIAL MEMBRANE PROTEASE-LIKE; INNER MITOCHONDRIAL MEMBRANE PEPTIDASE 2 LIKE. [RefSeq;Acc:NM_032549] 0.157677 0.725721 0.217269447 IMMP2L
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] no value
2436 0.0346049 0.159272 0.2172692 SETD3
2437 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] 0.171257 0.788327 0.217241069 ANAPC2
2438 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 0.12244 0.563645 0.21722893 BOLA2B
2439 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; 0.265861 1.22405 0.217197827 GGPS1
2440 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS). [SWISSPROT;Acc:P12081] 0.507204 2.33574 0.217149169 HARS
2441 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.0388043 0.178742 0.217096709 no value
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
2443 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.539817 2.48653 0.217096516 no value
2444 0.116413 0.536227 0.217096491 C7orf20
2445 0.0314703 0.14496 0.21709644 UBL4B
2446 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.109079 0.502445 0.217096399 no value
2447 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] 0.443267 2.0418 0.21709619 HARS2
2448 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] 0.205647 0.94731 0.21708522 ZMPSTE24
2449 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.0750119 0.345603 0.217046438 PGLS
2450 0.175357 0.808504 0.216890702 HDHD3

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/